# Patent

## Title
Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

## Abstract

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

## Background
RELATED APPLICATIONS
This application is a divisional of U.S. patent application Ser. No. 13/200,164, filed Sep. 20, 2011, pending, which is a divisional of U.S. patent application Ser. No. 13/066,645, filed Apr. 19, 2011, now U.S. Pat. No. 8,071,748, issued Dec. 6, 2011, which is a divisional of U.S. patent application Ser. No. 12/380,554, filed Feb. 26, 2009, now U.S. Pat. No. 7,960,534, issued Jun. 14, 2011, which application claims the benefit of the filing date of U.S. Provisional Patent Application Ser. No. 61/031,593, filed Feb. 26, 2008, for “THERMOPHILIC AND THERMOACIDOPHILIC SUGAR TRANSPORTER GENES AND ENZYMES FROM ALICYCLOBACILLUS ACIDOCALDARIUS AND RELATED ORGANISMS, METHODS,” the disclosure of each of which is hereby incorporated herein by this reference in its entirety.
STATEMENT ACCORDING TO 37 C.F.R. §1.821(c) OR (e)—SEQUENCE LISTING SUBMITTED AS ASCII TEXT FILE
Pursuant to 37 C.F.R. §1.821(c) or (e), a file containing an PDF version of the Sequence Listing has been submitted concomitant with this application, the contents of which are hereby incorporated by reference.


GOVERNMENT RIGHTS
This invention was made with government support under Contract No. DE-AC07-99ID13727 and Contract No. DE-AC07-05ID14517 awarded by the United States Department of Energy. The government has certain rights in the invention.


TECHNICAL FIELD
The present invention relates generally to biotechnology. More specifically, the present invention relates to isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and methods for their use.
BACKGROUND
Dilute acid hydrolysis to remove hemicellulose from lignocellulosic materials is one of the most developed pretreatment techniques for lignocellulose and is currently favored (Hamelinck et al., 2005) because it results in fairly high yields of xylose (75% to 90%). Conditions that are typically used range from 0.1% to 1.5% sulfuric acid and temperatures above 160° C. The high temperatures used result in significant levels of thermal decomposition products that inhibit subsequent microbial fermentations (Lavarack et al., 2002). High temperature hydrolysis requires pressurized systems, steam generation, and corrosion resistant materials in reactor construction due to the more corrosive nature of acid at elevated temperatures.
Low temperature acid hydrolyses are of interest because they have the potential to overcome several of the above shortcomings (Tsao et al., 1987). It has been demonstrated that 90% of hemicellulose can be solubilized as oligomers in a few hours of acid treatment in the temperature range of 80° C. to 100° C. It has also been demonstrated that the sugars produced in low temperature acid hydrolysis are stable under those same conditions for at least 24 hours with no detectable degradation to furfural decomposition products. Finally, sulfuric acid typically used in pretreatments is not as corrosive at lower temperatures. The use of lower temperature acid pretreatments requires much longer reaction times to achieve acceptable levels of hydrolysis. Although 90% hemicellulose solubilization has been shown (Tsao, 1987), the bulk of the sugars are in the form of oligomers and are not in the monomeric fowl. The organisms currently favored in subsequent fermentation steps cannot utilize sugar oligomers (Garrote et al., 2001) and the oligomer-containing hydrolysates require further processing to monomers, usually as a second acid or alkaline hydrolysis step (Garrote et al., 2001).
Other acidic pretreatment methods include autohydrolysis and hot water washing. In autohydrolysis, biomass is treated with steam at high temperatures ( ̃240° C.), which cleaves acetyl side chains associated with hemicellulose to produce acetic acid that functions in a similar manner to sulfuric acid in acid hydrolysis. Higher pretreatment temperatures are required as compared to dilute acid hydrolysis because acetic acid is a much weaker acid than sulfuric. At temperatures below 240° C., the hemicellulose is not completely hydrolyzed to sugar monomers and has high levels of oligomers (Garrote et al., 2001). In hot water washing, biomass is contacted with water (under pressure) at elevated temperatures 160° C. to 220° C. This process can effectively hydrolyze greater than 90% of the hemicellulose present and the solubilized hemicellulose was typically over 95% in the form of oligomers (Liu and Wyman, 2003).
BRIEF SUMMARY OF THE INVENTION
Embodiments of the invention relate to purified and/or isolated nucleotide sequences of the genome of Alicyclobacillus acidocaldarius, or a homologue or fragment thereof. In one embodiment of the invention, the nucleotide sequence is selected from at least one of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 or a homologue or fragment thereof. In another embodiment of the invention, the homologue is selected from the group consisting of a nucleotide sequence having at least 80% sequence identity to at least one of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767.
Embodiments of the invention may further relate to an isolated and/or purified nucleic acid sequence comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of a polypeptide having at least 90% sequence identity to at least one of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766.
Embodiments of the invention also relate to isolated and/or purified polypeptides coded for by a nucleotide sequence comprising a nucleotide sequence of the genome of Alicyclobacillus acidocaldarius, or a homologue or fragment thereof. In one embodiment, the nucleotide sequence comprises a nucleotide sequence selected from the group consisting of a nucleotide sequence having at least 80% sequence identity to at least one of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767.
In another embodiment of the invention, the nucleotide sequence comprises a nucleotide sequence selected from at least one of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 or a homologue or fragment thereof. In still another embodiment, the polypeptide comprises an amino acid sequence of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766. In yet another embodiment, the polypeptide comprises an amino acid sequence selected from the group consisting of a polypeptide having at least 90% sequence identity to at least one of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766.
In embodiments of the invention, the polypeptides may be acidophilic and/or thermophilic. In further embodiments, the polypeptides may be glycosylated, pegylated, and/or otherwise post-translationally modified.
Embodiments of methods include providing a recombinant, purified, and/or isolated polypeptide selected from the group consisting of a polypeptide having at least 90% sequence identity to SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 in or associated with a cell membrane and transporting a sugar across the cell membrane using the a recombinant, purified, and/or isolated polypeptide in conjunction with other cellular components.
Further embodiments of methods include placing a cell producing or encoding a recombinant, purified, and/or isolated nucleotide sequence comprising a nucleotide sequence selected from the group consisting of a nucleotide sequences having at least 90% sequence identity to at least one of the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 and/or a recombinant, purified, and/or isolated polypeptide selected from the group consisting of a polypeptide having at least 90% sequence identity to at least one of the sequences of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 in a environment comprising temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/or a pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0.
These and other aspects of the invention will become apparent to the skilled artisan in view of the teachings contained herein.



BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
FIG. 1 depicts a sequence alignment between SEQ ID NO:1 (RAAC00572) and emb|CAB65652.1|, ref|NP—623417.1|, ref|YP—001662812.1|, ref|YP—001179257.1|, and ref|YP—699602.1|(SEQ ID NOS:3-7), respectively, which all have the function assigned to SEQ ID NO:1 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 2A and 2B depict a sequence alignment between SEQ ID NO:18 (RAAC00573) and emb|CAB65651.1|, pdb|1URG|A, pdb|1URD|A, ref|YP—001662811.1|, and ref|NP—623418.1|(SEQ ID NOS:20-24), respectively, which all have the function assigned to SEQ ID NO:18 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 3A and 3B depict a sequence alignment between SEQ ID NO:35 (RAAC00608) and ref|NP—391276.1|, ref|YP—001422694.1|, ref|NP—347967.1|, ref|ZP—01886765.1|, and ref|YP—804553.1| (SEQ ID NOS:37-41), respectively, which all have the function assigned to SEQ ID NO:35 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 4A and 4B depict a sequence alignment between SEQ ID NO:52 (RAAC00626) and ref|YP—001108359.1|, ref|YP—001662045.1|, ref|YP—147976.1|, ref|YP—001126119.1|, and ref|YP—001409972.1| (SEQ ID NOS:54-58), respectively, which all have the function assigned to SEQ ID NO:52 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 5 depicts a sequence alignment between SEQ ID NO:69 (RAAC00627) and ref|YP—001108360.1|, ref|ZP—01730302.1|, ref|YP—001662044.1|, ref|YP—171303.1|, and ref|YP—922080.1| (SEQ ID NOS:71-75), respectively, which all have the function assigned to SEQ ID NO:69 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 6 depicts a sequence alignment between SEQ ID NO:86 (RAAC00628) and ref|YP—001108361.1|, ref|YP—001662043.1|, ref|YP—147974.1|, ref|YP—001126117.1|, and ref|NP—694394.1| (SEQ ID NOS:88-92), respectively, which all have the function assigned to SEQ ID NO:86 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 7A and 7B depict a sequence alignment between SEQ ID NO:103 (RAAC00662) and ref|YP—644805.1|, ref|YP—589403.1|, ref|YP—822512.1|, ref|YP—825097.1|, and ref|YP—001108350.1|(SEQ ID NOS:105-109), respectively, which all have the function assigned to SEQ ID NO:103 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 8 depicts a sequence alignment between SEQ ID NO:120 (RAAC00732) and emb|CAE45698.1|, ref|ZP—02329051.1|, ref|YP—001181115.1|, ref|NP—623554.1|, and ref|YP—001664561.1| (SEQ ID NOS:122-126), respectively, which all have the function assigned to SEQ ID NO:120 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 9A and 9B depict a sequence alignment between SEQ ID NO:137 (RAAC00804) and ref|NP—623507.1|, ref|YP—001469682.1|, ref|YP—145275.1|, ref|YP—006204.1|, and ref|YP—001432292.1| (SEQ ID NOS:139-143), respectively, which all have the function assigned to SEQ ID NO:137 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 10A and 10B depict a sequence alignment between SEQ ID NO:154 (RAAC00824) and ref|ZP—02128903.1|, ref|YP—001243927.1|, ref|YP—001390862.1|, ref|YP—001254028.1|, and ref|NP—228405.1| (SEQ ID NOS:156-160), respectively, which all have the function assigned to SEQ ID NO:154 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 11A and 11B depict a sequence alignment between SEQ ID NO:171 (RAAC01073) and ref|YP—804553.1|, ref|NP—391276.1|, ref|YP—001422694.1|, ref|NP 347967.1|, and ref|NP—978526.1|(SEQ ID NOS:173-177), respectively, which all have the function assigned to SEQ ID NO:171 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 12A and 12B depict a sequence alignment between SEQ ID NO:188 (RAAC01120) and ref|YP—001089934.1|, ref|ZP—01801573.1|, ref|ZP—01173000.1|, ref|YP—076008.1|, and gb|ABP—57783.1| (SEQ ID NOS:190-194), respectively, which all have the function assigned to SEQ ID NO:188 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 13 depicts a sequence alignment between SEQ ID NO:205 (RAAC01122) and ref|YP—001527659.1|, ref|YP—321082.1|, ref|NP—484832.1|, ref|ZP—01631485.1|, and gb|AAD33665.1|AF135398—2 (SEQ ID NOS:207-211), respectively, which all have the function assigned to SEQ ID NO:205 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 14 depicts a sequence alignment between SEQ ID NO:222 (RAAC01168) and ref|ZP—02083881.1|, ref|ZP—02075264.1|, ref|ZP—01461962.1|, ref|YP—632791.1|, and ref|NP—348945.1| (SEQ ID NOS:224-228), respectively, which all have the function assigned to SEQ ID NO:222 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 15 depicts a sequence alignment between SEQ ID NO:239 (RAAC01169) and ref|ZP—02075265.1|, ref|ZP—02083878.1|, ref|ZP—02085002.1|, ref|ZP—01978997.1|, and ref|ZP—02045164.1| (SEQ ID NOS:241-245), respectively, which all have the function assigned to SEQ ID NO:239 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 16 depicts a sequence alignment between SEQ ID NO:256 (RAAC01276) and ref|YP—173899.1|, ref|NP 241985.1|, ref|ZP—01168682.1|, ref|ZP—02087132.1|, and ref|YP—173890.1| (SEQ ID NOS:258-262), respectively, which all have the function assigned to SEQ ID NO:256 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 17 depicts a sequence alignment between SEQ ID NO:273 (RAAC01277) and ref|YP—949009.1|, ref|YP—73889.1|, ref|YP—001361891.1|, ref|YP—832803.1|, and ref|ZP—01168681.1| (SEQ ID NOS:275-279), respectively, which all have the function assigned to SEQ ID NO:273 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 18A and 18B depict a sequence alignment between SEQ ID NO:290 (RAAC01278) and ref|YP—289760.1|, ref|NP—241983.1|, ref|YP—173897.1|, ref|YP—173888.1|, and ref|NP—357484.21 (SEQ ID NOS:292-296), respectively, which all have the function assigned to SEQ ID NO:290 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 19 depicts a sequence alignment between SEQ ID NO:307 (RAAC01279) and ref|NP—693016.1|, ref|ZP—01924075.1|, ref|YP—74646.1|, ref|ZP—01854967.1|, and ref|ZP—01088898.1| (SEQ ID NOS:309-313), respectively, which all have the function assigned to SEQ ID NO:307 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 20A and 20B depict a sequence alignment between SEQ ID NO:324 (RAAC01316) and ref|YP—001523023.1|, ref|ZP—01746012.1|, ref|YP—001479789.1|, ref|YP—001585330.1|, and ref|NP—845565.1| (SEQ ID NOS:326-330), respectively, which all have the function assigned to SEQ ID NO:324 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 21 depicts a sequence alignment between SEQ ID NO:341 (RAAC01502) and ref|YP—001113858.1|, ref|ZP—02171111.1|, ref|YP—001488480.1|, ref|YP—878667.1|, and ref|NP—693494.1| (SEQ ID NOS:343-347), respectively, which all have the function assigned to SEQ ID NO:341 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 22 depicts a sequence alignment between SEQ ID NO:358 (RAAC01599) and ref|YP—114375.1|, ref|YP—001568000.1|, ref|YP—001254026.1|, ref|YP—001390860.1|, and ref|YP—001275707.1|(SEQ ID NOS:360-364), respectively, which all have the function assigned to SEQ ID NO:358 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 23A and 23B depict a sequence alignment between SEQ ID NO:375 (RAAC01600) and ref YP—076008.1|, ref|YP—001624170.1|, ref|YP—001089934.1|, ref|ZP—01801573.1|, and ref|ZP—01850509.1| (SEQ ID NOS:377-381), respectively, which all have the function assigned to SEQ ID NO:375 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 24 depicts a sequence alignment between SEQ ID NO:392 (RAAC01625) and ref|YP—001527658.1|, ref|ZP—01189621.1|, ref|YP—001327980.1|, ref|NP—436764.1|, and ref|NP 463711.1| (SEQ ID NOS:394-398), respectively, which all have the function assigned to SEQ ID NO:392 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 25A and 25B depict a sequence alignment between SEQ ID NO:409 (RAAC01626) and ref|YP—001624853.1|, ref|YP—832862.1|, ref|NP—733496.1|, ref|NP—961026.1|, and ref|YP—881303.1|(SEQ ID NOS:411-415), respectively, which all have the function assigned to SEQ ID NO:409 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 26 depicts a sequence alignment between SEQ ID NO:426 (RAAC01627) and ref|ZP—01115262.1|, ref|NP—815894.1|, ref|YP—173820.1|, ref|NP—624601.1|, and ref|NP 336858.1| (SEQ ID NOS:428-432), respectively, which all have the function assigned to SEQ ID NO:426 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 27A and 27B depict a sequence alignment between SEQ ID NO:443 (RAAC01754) and ref|ZP—01172341.1|, ref|YP—001665505.1|, ref|YP—001663811.1|, ref|YP—001124945.1|, and ref|NP—622450.1| (SEQ ID NOS:445-449), respectively, which all have the function assigned to SEQ ID NO:443 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 28A and 28B depict a sequence alignment between SEQ ID NO:460 (RAAC01756) and ref|YP—001665503.1|, ref|NP—622452.1|, ref|YP—001179269.1|, ref|YP—001124947.1|, and ref|NP 244557.1| (SEQ ID NOS:462-466), respectively, which all have the function assigned to SEQ ID NO:460 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 29 depicts a sequence alignment between SEQ ID NO:477 (RAAC01757) and ref|YP—001665502.1|, ref|YP—001663808.1|, ref|NP—622453.1|, ref|ZP—01172344.1|, and ref|YP—001179270.1| (SEQ ID NOS:479-483), respectively, which all have the function assigned to SEQ ID NO:477 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 30 depicts a sequence alignment between SEQ ID NO:494 (RAAC01758) and ref|NP—622454.1|, ref|YP—001665501.1|, ref|YP—001663807.1|, ref|YP—001179271.1|, and ref|YP—001124949.1| (SEQ ID NOS:496-500), respectively, which all have the function assigned to SEQ ID NO:494 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 31A and 31B depict a sequence alignment between SEQ ID NO:511 (RAAC01989) and ref|YP—001614945.1|, ref|YP—001619074.1|, ref|YP—001618197.1|, ref|YP—001471644.1|, and ref|YP—001613999.1| (SEQ ID NOS:513-517), respectively, which all have the function assigned to SEQ ID NO:511 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 32 depicts a sequence alignment between SEQ ID NO:528 (RAAC01990) and ref|YP—829900.1|, ref|YP—947699.1|, ref|YP—001032750.1|, ref|YP—001614944.1|, and ref|YP—001545164.1| (SEQ ID NOS:530-534), respectively, which all have the function assigned to SEQ ID NO:528 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 33 depicts a sequence alignment between SEQ ID NO:545 (RAAC01991) and ref|YP—001032749.1|, ref|YP—001567539.1|, ref|YP—614737.1|, ref|YP—001471642.1|, and ref|YP—063070.1| (SEQ ID NOS:547-551), respectively, which all have the function assigned to SEQ ID NO:545 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 34 depicts a sequence alignment between SEQ ID NO:562 (RAAC01992) and ref|YP—001614942.1|, ref|YP—001545162.1|, ref|ZP—01473687.1|, ref|NP—798861.1|, and ref|ZP—01262242.1| (SEQ ID NOS:564-568), respectively, which all have the function assigned to SEQ ID NO:562 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 35 depicts a sequence alignment between SEQ ID NO:579 (RAAC02175) and ref|YP—644454.1|, ref|ZP—00133639.21, ref|YP—001337166.1|, ref|YP—001591175.1|, and ref|YP—355005.1| (SEQ ID NOS:581-585), respectively, which all have the function assigned to SEQ ID NO:579 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 36 depicts a sequence alignment between SEQ ID NO:596 (RAAC02176) and ref|ZP—01440479.1|, gb|EDR95515.1|, ref|YP—037038.1|, ref|ZP—02260050.1|, and ref|YP—029022.1| (SEQ ID NOS:598-602), respectively, which all have the function assigned to SEQ ID NO:596 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 37 depicts a sequence alignment between SEQ ID NO:613 (RAACO02177) and ref|NP—832709.1|, ref|YP—001565594.1|, ref|ZP—00239479.1|, ref|YP—001178244.1|, and ref|YP—001337168.1|(SEQ ID NOS:615-619), respectively, which all have the function assigned to SEQ ID NO:613 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 38A and 38B depict a sequence alignment between SEQ ID NO:630 (RAAC02613) and ref|YP—001546405.1|, ref|ZP—02171436.1|, ref|ZP—02295559.1|, ref|YP—765572.1|, and ref|NP 106947.1| (SEQ ID NOS:632-636), respectively, which all have the function assigned to SEQ ID NO:630 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 39 depicts a sequence alignment between SEQ ID NO:647 (RAAC02614) and gb|AAD33665.1|AF135398—2, dbj|BAA28360.1|, ref|ZP—02016963.1|, ref|YP—765571.1|, and ref|NP—357451.21 (SEQ ID NOS:649-653), respectively, which all have the function assigned to SEQ ID NO:647 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 40 depicts a sequence alignment between SEQ ID NO:664 (RAAC02615) and ref|ZP—02171438.1|, ref|ZP—02016964.1|, ref|ZP—01188237.1|, ref|YP—176793.1|, and ref|YP—001546403.1|(SEQ ID NOS:666-670), respectively, which all have the function assigned to SEQ ID NO:664 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 41 depicts a sequence alignment between SEQ ID NO:681 (RAAC02733) and ref|YP—001179080.1|, ref|NP—244315.1|, ref|YP—147766.1|, ref|YP—001125909.1|, and ref|YP—077677.1| (SEQ ID NOS:683-687), respectively, which all have the function assigned to SEQ ID NO:681 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 42 depicts a sequence alignment between SEQ ID NO:698 (RAAC02734) and ref|YP—001179079.1|, ref|YP—001036823.1|, ref|YP—001312352.1|, ref|NP 437024.1|, and ref|YP—471845.1| (SEQ ID NOS:700-704), respectively, which all have the function assigned to SEQ ID NO:968 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 43 depicts a sequence alignment between SEQ ID NO:715 (RAAC04053) and ref|YP—001235093.1|, ref|YP—001547100.1|, ref|ZP—01464237.1|, ref|YP—001509451.1|, and ref|YP—430861.1| (SEQ ID NOS:717-721), respectively, which all have the function assigned to SEQ ID NO:715 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 44 depicts a sequence alignment between SEQ ID NO:732 (RAAC04054) and ref|YP—001547099.1|, gb|AAK01295.1|AF332585—1, ref|YP—001235092.1|, ref|YP—289977.1|, and ref|NP 823422.1|(SEQ ID NOS:734-738), respectively, which all have the function assigned to SEQ ID NO:732 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIG. 45 depicts a sequence alignment between SEQ ID NO:749 (RAAC04055) and ref|YP—001547098.1|, ref|ZP—01464218.1|, ref|YP—001509449.1|, ref|YP—001235091.1|, and ref|YP—289976.1| (SEQ ID NOS:751-755), respectively, which all have the function assigned to SEQ ID NO:749 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.
FIGS. 46A and 46B depict a sequence alignment between SEQ ID NO:766 (RAAC03004) and ref|YP—001234214.1|, ref|NP—343451.1|, ref|YP—256381.1|, ref|NP 376612.1|, and ref|YP—001191851.1| (SEQ ID NOS:768-772), respectively, which all have the function assigned to SEQ ID NO:766 in Table 1. Amino acids conserved among all sequences are indicated by a “*” and generally conserved amino acids are indicated by a “:”.



DETAILED DESCRIPTION OF THE INVENTION
Lignocellulose is a highly heterogeneous three-dimensional matrix comprised primarily of cellulose, hemicellulose, and lignin. Many fuels and chemicals can be made from these lignocellulosic materials. To utilize lignocellulosic biomass for production of fuels and chemicals via fermentative processes, it is necessary to convert the plant polysaccharides to sugar monomers, which are then fermented to products using a variety of microorganisms. Direct hydrolysis of lignocellulose by mineral acids to monomers is possible at high temperatures and pressures, leading to yield losses due to thermal decomposition of the sugars. Utilizing existing commercially available enzymes, a first strategy to reduce these yield losses is to perform the pretreatment at a reduced severity to produce soluble oligomers, followed by the use of use cellulases and hemicellulases to depolymerize the polysaccharides at moderate temperatures. In a second approach, the addition of acid stable thermotolerant hydrolytic enzymes including cellulases, xylanases and other hemicellulases to the biomass slurry during the pretreatment allows the use of further reduced temperatures and pressures during the pretreatment, as well as cheaper materials of construction, reducing both the capital and energy costs. An extension of this second approach is to combine the enzyme-assisted reduced severity pretreatment together with fermentation under the same conditions, which further reduces costs.
Regardless of which approach is used, sugars generated by the approach may be used by cells to create useful fuels and chemicals, such, by way of non-limiting example, ethanol. Thus, transporters that function in low pH and/or high temperatures are useful to transport the generated sugars from the extracellular medium into a cell for secondary processing into a material of interest.
Embodiments of the invention include genes and associated proteins related to the metabolism and sugar transport of the thermoacidophile Alicyclobacillus acidocaldarius. Coding sequences for genes related to these processes were determined from sequence information generated from sequencing the genome of Alicyclobacillus acidocaldarius. These genes and proteins may represent targets for metabolic engineering of Alicyclobacillus acidocaldarius or other organisms. Non-limiting examples of nucleotide sequences found within the genome of Alicyclobacillus acidocaldarius, and amino acids coded thereby, associated with sugar transport are listed in Table 1. Sugar transporters and associated molecules may be, without limitation, of the following classes: glucose, galactose, xylose, mannose, arabinose, maltose, lactose, ribose, uronic acids formed from these sugars, acetylated sugars from the aforementioned classes, soluble saccharides of these sugars including dimers, trimers, and larger oligomers of the sugars both singly and in combination, transporters and associated molecules, saccharide transporters and associated molecules; polysaccharide and/or oligosaccharide transporters and associated molecules; cyclodextrin, melibiose, cellobiose, galacturonate, oligogalactouronate, glucarate, polyol, chitooligosaccharide, transporters and associated molecules; polyABC-type sugar transport systems, permease components; Maltose-binding periplasmic proteins/domains; Cyclodextrin-binding proteins; Arabinose/Xylose/Galactose permeases; Sodium-glucose/galactose cotransporters; ABC-type sugar transport systems, ATPase components; Na+/melibiose symporters and related transporters; ABC-type sugar transport system, periplasmic components; Arabinose/Xylose/Galactose permeases; Sugar binding proteins/transporters; ABC-type polysaccharide/polyol phosphate export systems, permease components; ABC-type polysaccharide/polyol phosphate transport systems, ATPase components; ABC-type Oligogalacturonate transport system permease protein OgtB; ABC-type Oligogalacturonate transport system permease protein OgtA; ABC-type Oligogalacturonate-binding protein OgtD, periplasmic components; Glucarate/galactarate transporters; Ribose transport system permease protein rbsC; Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; ABC-type sugar transport system/extracellular sugar binding proteins, periplasmic components; Cellobiose transporters or regulators; Sugar-binding proteins; Oligosaccharide binding proteins; ABC oligosaccharide transporters; ABC oligosaccharide permeases/transporters; ABC chitooligosaccharide transporters; Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; ABC-type sugar transport system, periplasmic components; Lactose-binding proteins; Lactose transport system permease protein lacF; D-ribose-binding proteins; Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; ABC-type xylose transport system, periplasmic components; D-xylose-binding proteins; D-xylose transport ATP-binding protein xylG; ABC-type xylose transport system, permease components; xylH; D-Xylose proton-symporters; and Sugar kinase activities; and others.
Embodiments of the invention relate in part to the gene sequences and/or protein sequences comprising genes and/or proteins of Alicyclobacillus acidocaldarius. Genes and proteins included are those that play a role in sugar transport. Intracellular enzyme activities may be thermophilic and/or acidophilic in nature and general examples of similar genes are described in the literature. Classes of genes, sequences, enzymes and factors include, but are not limited to, those listed in Table 1.







TABLE 1







Alicyclobacillus acidocaldarius genes and proteins related to sugar transport











Protein




Reference
Sequence
Gene Sequence
Function





RAAC00572
SEQ ID NO: 1
SEQ ID NO: 2
ABC-type sugar transport systems, permease components


RAAC00573
SEQ ID NO: 18
SEQ ID NO: 19
Maltose-binding periplasmic proteins/domains;





Cyclodextrin-binding protein


RAAC00608
SEQ ID NO: 35
SEQ ID NO: 36
Arabinose/Xylose/Galactose permease


RAAC00626
SEQ ID NO: 52
SEQ ID NO: 53
ABC-type sugar transport system, periplasmic component


RAAC00627
SEQ ID NO: 69
SEQ ID NO: 70
ABC-type sugar transport systems, permease components


RAAC00628
SEQ ID NO: 86
SEQ ID NO: 87
ABC-type sugar transport system, permease component


RAAC00662
SEQ ID NO: 103
SEQ ID NO: 104
Sodium-glucose/galactose cotransporter


RAAC00732
SEQ ID NO: 120
SEQ ID NO: 121
ABC-type sugar transport systems, ATPase components


RAAC00804
SEQ ID NO: 137
SEQ ID NO: 138
Na+/melibiose symporter and related transporters


RAAC00824
SEQ ID NO: 154
SEQ ID NO: 155
ABC-type sugar transport system, periplasmic component


RAAC01073
SEQ ID NO: 171
SEQ ID NO: 172
Arabinose/Xylose/Galactose permease


RAAC01120
SEQ ID NO: 188
SEQ ID NO: 189
Sugar binding protein/transport


RAAC01122
SEQ ID NO: 205
SEQ ID NO: 206
ABC-type sugar transport systems, permease components


RAAC01168
SEQ ID NO: 222
SEQ ID NO: 223
ABC-type polysaccharide/polyol phosphate export systems,





permease component


RAAC01169
SEQ ID NO: 239
SEQ ID NO: 240
ABC-type polysaccharide/polyol phosphate transport system,





ATPase component


RAAC01276
SEQ ID NO: 256
SEQ ID NO: 257
ABC-type Oligogalacturonate transport system permease





protein OgtB


RAAC01277
SEQ ID NO: 273
SEQ ID NO: 274
ABC-type Oligogalacturonate transport system permease





protein OgtA


RAAC01278
SEQ ID NO: 290
SEQ ID NO: 291
ABC-type Oligogalacturonate-binding protein OgtD,





periplasmic component


RAAC01279
SEQ ID NO: 307
SEQ ID NO: 308
ABC-type sugar transport system, periplasmic component


RAAC01316
SEQ ID NO: 324
SEQ ID NO: 325
Glucarate/galactarate transporter


RAAC01502
SEQ ID NO: 341
SEQ ID NO: 342
Ribose transport system permease protein rbsC;





Ribose/xylose/arabinose/galactoside ABC-type transport





systems, permease components


RAAC01599
SEQ ID NO: 358
SEQ ID NO: 359
ABC-type sugar transport systems, permease components


RAAC01600
SEQ ID NO: 375
SEQ ID NO: 376
ABC-type sugar transport system, periplasmic component


RAAC01625
SEQ ID NO: 392
SEQ ID NO: 393
ABC-type sugar transport system, permease component


RAAC01626
SEQ ID NO: 409
SEQ ID NO: 410
ABC-type sugar transport system/extracellular sugar binding





protein, periplasmic component


RAAC01627
SEQ ID NO: 426
SEQ ID NO: 427
ABC-type sugar transport systems, permease components


RAAC01754
SEQ ID NO: 443
SEQ ID NO: 444
Cellobiose transport or regulator


RAAC01756
SEQ ID NO: 460
SEQ ID NO: 461
ABC-type sugar transport system, periplasmic component;





Sugar-binding protein


RAAC01757
SEQ ID NO: 477
SEQ ID NO: 478
ABC-type sugar transport systems, permease components


RAAC01758
SEQ ID NO: 494
SEQ ID NO: 495
ABC-type sugar transport system, permease component


RAAC01989
SEQ ID NO: 511
SEQ ID NO: 512
Oligosaccharide binding protein


RAAC01990
SEQ ID NO: 528
SEQ ID NO: 529
ABC oligosaccharide transport


RAAC01991
SEQ ID NO: 545
SEQ ID NO: 546
ABC oligosaccharide permease/transport


RAAC01992
SEQ ID NO: 562
SEQ ID NO: 563
ABC chitooligosaccharide transport


RAAC02175
SEQ ID NO: 579
SEQ ID NO: 580
ABC-type sugar transport system, periplasmic component


RAAC02176
SEQ ID NO: 596
SEQ ID NO: 597
Ribose/xylose/arabinose/galactoside ABC-type transport





systems, permease components


RAAC02177
SEQ ID NO: 613
SEQ ID NO: 614
Ribose/xylose/arabinose/galactoside ABC-type transport





systems, permease components


RAAC02613
SEQ ID NO: 630
SEQ ID NO: 631
ABC-type sugar transport system, periplasmic component;





Lactose-binding protein


RAAC02614
SEQ ID NO: 647
SEQ ID NO: 648
ABC-type sugar transport systems, permease components;





Lactose transport system permease protein lacF


RAAC02615
SEQ ID NO: 664
SEQ ID NO: 665
ABC-type sugar transport system, permease component


RAAC02733
SEQ ID NO: 681
SEQ ID NO: 682
ABC-type sugar transport system, periplasmic component;





D-ribose-binding protein


RAAC02734
SEQ ID NO: 698
SEQ ID NO: 699
Ribose/xylose/arabinose/galactoside ABC-type transport





systems, permease components


RAAC04053
SEQ ID NO: 715
SEQ ID NO: 716
ABC-type xylose transport system, periplasmic component;





D-xylose-binding protein


RAAC04054
SEQ ID NO: 732
SEQ ID NO: 733
D-xylose transport ATP-binding protein xylG


RAAC04055
SEQ ID NO: 749
SEQ ID NO: 750
ABC-type xylose transport system, permease component; xylH


RAAC03004
SEQ ID NO: 766
SEQ ID NO: 767
D-XYLOSE PROTON-SYMPORTER; Predicted sugar kinase









The present invention relates to nucleotides sequences comprising isolated and/or purified nucleotide sequences of the genome of Alicyclobacillus acidocaldarius selected from the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767, or one of their fragments.
The present invention likewise relates to isolated and/or purified nucleotide sequences, characterized in that they comprise at least one of: a) a nucleotide sequence of at least one of the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 or one of their fragments; b) a nucleotide sequence homologous to a nucleotide sequence such as defined in a); c) a nucleotide sequence complementary to a nucleotide sequence such as defined in a) or b), and a nucleotide sequence of their corresponding RNA; d) a nucleotide sequence capable of hybridizing under stringent conditions with a sequence such as defined in a), b) or c); e) a nucleotide sequence comprising a sequence such as defined in a), b), c) or d); and f) a nucleotide sequence modified by a nucleotide sequence such as defined in a), b), c), d) or e).
Nucleotide, polynucleotide, or nucleic acid sequence will be understood according to the present invention as meaning both a double-stranded or single-stranded DNA in the monomeric and dimeric (so-called in tandem) forms and the transcription products of the DNAs.
Aspects of the invention relate nucleotide sequences, which it has been possible to isolate, purify or partially purify, starting from separation methods such as, for example, ion-exchange chromatography, by exclusion based on molecular size, or by affinity, or alternatively fractionation techniques based on solubility in different solvents, or starting from methods of genetic engineering such as amplification, cloning, and subcloning, it being possible for the sequences of the invention to be carried by vectors.
Isolated and/or purified nucleotide sequence fragment according to the invention will be understood as designating any nucleotide fragment of the genome of Alicyclobacillus acidocaldarius, and may include, by way of non-limiting examples, length of at least 8, 12, 20 25, 50, 75, 100, 200, 300, 400, 500, 1000, or more, consecutive nucleotides of the sequence from which it originates.
Specific fragment of an isolated and/or purified nucleotide sequence according to the invention will be understood as designating any nucleotide fragment of the genome of Alicyclobacillus acidocaldarius, having, after alignment and comparison with the corresponding fragments of genomic sequences of Alicyclobacillus acidocaldarius, at least one nucleotide or base of different nature.
Homologous isolated and/or purified nucleotide sequence, in the sense of the present invention, is understood as meaning isolated and/or purified a nucleotide sequence having at least a percentage identity with the bases of a nucleotide sequence according to the invention of at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7%, this percentage being purely statistical and it being possible to distribute the differences between the two nucleotide sequences at random and over the whole of their length.
Specific homologous nucleotide sequence in the sense of the present invention is understood as meaning a homologous nucleotide sequence having at least one nucleotide sequence of a specific fragment, such as defined above. The “specific” homologous sequences can comprise, for example, the sequences corresponding to the genomic sequence or to the sequences of its fragments representative of variants of the genome of Alicyclobacillus acidocaldarius. These specific homologous sequences can thus correspond to variations linked to mutations within strains of Alicyclobacillus acidocaldarius, and especially correspond to truncations, substitutions, deletions and/or additions of at least one nucleotide. The homologous sequences can likewise correspond to variations linked to the degeneracy of the genetic code.
The term “degree or percentage of sequence homology” refers to “degree or percentage of sequence identity between two sequences after optimal alignment” as defined in the present application.
Two amino-acids or nucleotidic sequences are said to be “identical” if the sequence of amino-acids or nucleotidic residues, in the two sequences is the same when aligned for maximum correspondence as described below. Sequence comparisons between two (or more) peptides or polynucleotides are typically performed by comparing sequences of two optimally aligned sequences over a segment or “comparison window” to identify and compare local regions of sequence similarity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman, Ad. App. Math 2:482 (1981), by the homology alignment algorithm of Neddleman and Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. (U.S.A.) 85:2444 (1988), by computerized implementation of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by visual inspection.
“Percentage of sequence identity” (or degree of identity) is determined by comparing two optimally aligned sequences over a comparison window, where the portion of the peptide or polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical amino-acid residue or nucleic acid base occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
The definition of “sequence identity,” given above, is the definition that would be used by one of skill in the art. The definition by itself does not need the help of any algorithm, the algorithms being helpful only to achieve the optimal alignments of sequences, rather than the calculation of sequence identity.
From the definition given above, it follows that there is a well-defined and only one value for the sequence identity between two compared sequences which value corresponds to the value obtained for the best or optimal alignment.
In the BLAST N or BLAST P “BLAST 2 sequence” software, which is available on the Internet from the web site ncbi.nlm.nih.gov/gorf/bl2.html, and habitually used by the inventors and in general by the skilled person for comparing and determining the identity between two sequences, gap cost that depends on the sequence length to be compared is directly selected by the software (i.e., 11.2 for substitution matrix BLOSUM-62 for length>85).
Complementary nucleotide sequence of a sequence of the invention is understood as meaning any DNA whose nucleotides are complementary to those of the sequence of the invention, and whose orientation is reversed (antisense sequence).
Hybridization under conditions of stringency with a nucleotide sequence according to the invention is understood as meaning hybridization under conditions of temperature and ionic strength chosen in such a way that they allow the maintenance of the hybridization between two fragments of complementary DNA.
By way of illustration, conditions of great stringency of the hybridization step with the aim of defining the nucleotide fragments described above are advantageously the following.
The hybridization is carried out at a preferential temperature of 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15 M NaCl and 0.05 M Na citrate. The washing steps, for example, can be the following: 2×SSC, at ambient temperature followed by two washes with 2×SSC, 0.5% SDS at 65° C.; 2×0.5×SSC, 0.5% SDS; at 65° C. for 10 minutes each.
The conditions of intermediate stringency, using, for example, a temperature of 42° C. in the presence of a 2×SSC buffer, or of less stringency, for example, a temperature of 37° C. in the presence of a 2×SSC buffer, respectively require a globally less significant complementarity for the hybridization between the two sequences.
The stringent hybridization conditions described above for a polynucleotide with a size of approximately 350 bases will be adapted by a person skilled in the art for oligonucleotides of greater or smaller size, according to the teaching of Sambrook et al., 1989.
Among the isolated and/or purified nucleotide sequences according to the invention, are those that can be used as a primer or probe in methods allowing the homologous sequences according to the invention to be obtained, these methods, such as the polymerase chain reaction (PCR), nucleic acid cloning, and sequencing, being well known to the person skilled in the art.
Among the isolated and/or purified nucleotide sequences according to the invention, those are again preferred that can be used as a primer or probe in methods allowing the presence of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767, one of their fragments, or one of their variants such as defined below to be diagnosed.
The nucleotide sequence fragments according to the invention can be obtained, for example, by specific amplification, such as PCR, or after digestion with appropriate restriction enzymes of nucleotide sequences according to the invention, these methods in particular being described in the work of Sambrook et al., 1989. Such representative fragments can likewise be obtained by chemical synthesis according to methods well known to persons of ordinary skill in the art.
“Modified nucleotide sequence” will be understood as meaning any nucleotide sequence obtained by mutagenesis according to techniques well known to the person skilled in the art, and containing modifications with respect to the normal sequences according to the invention, for example mutations in the regulatory and/or promoter sequences of polypeptide expression, especially leading to a modification of the rate of expression of the polypeptide or to a modulation of the replicative cycle.
“Modified nucleotide sequence” will likewise be understood as meaning any nucleotide sequence coding for a modified polypeptide such as defined below.
The present invention relates to nucleotide sequence comprising isolated and/or purified nucleotide sequences of Alicyclobacillus acidocaldarius, characterized in that they are selected from the sequences SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 or one of their fragments.
Embodiments of the invention likewise relate to isolated and/or purified nucleotide sequences characterized in that they comprise a nucleotide sequence selected from: a) at least one of a nucleotide sequence of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 or one of their fragments or one of their fragments; b) a nucleotide sequence of a specific fragment of a sequence such as defined in a); c) a homologous nucleotide sequence having at least 80% identity with a sequence such as defined in a) or b); d) a complementary nucleotide sequence or sequence of RNA corresponding to a sequence such as defined in a), b) or c); and e) a nucleotide sequence modified by a sequence such as defined in a), b), c) or d).
Among the isolated and/or purified nucleotide sequences according to the invention are the nucleotide sequences of SEQ ID NOS:13-17, 30-34, 47-51, 64-68, 81-85, 98-102, 115-119, 132-136, 149-153, 166-170, 183-187, 200-204, 217-221, 234-238, 251-255, 268-272, 285-289, 302-306, 319-323, 336-340, 353-357, 370-374, 387-391, 404-408, 421-425, 438-442, 455-459, 472-476, 489-493, 506-510, 523-527, 540-544, 557-561, 574-578, 591-595, 608-612, 625-629, 642-646, 659-663, 676-680, 693-697, 710-714, 727-731, 744-748, 761-765, and 778-782, or fragments thereof and any isolated and/or purified nucleotide sequences, which have a homology of at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7% identity with the at least one of the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 or fragments thereof. The homologous sequences can comprise, for example, the sequences corresponding to the genomic sequences Alicyclobacillus acidocaldarius. In the same manner, these specific homologous sequences can correspond to variations linked to mutations within strains of Alicyclobacillus acidocaldarius and especially correspond to truncations, substitutions, deletions and/or additions of at least one nucleotide. As will be apparent to one of ordinary skill in the art, such homologues are easily created and identified using standard techniques and publicly available computer programs such as BLAST. As such, each homologue referenced above should be considered as set forth herein and fully described.
Embodiments of the invention comprise the isolated and/or purified polypeptides coded for by a nucleotide sequence according to the invention, or fragments thereof, whose sequence is represented by a fragment. Amino acid sequences corresponding to the isolated and/or purified polypeptides, which can be coded for according to one of the three possible reading frames of at least one of the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767.
Embodiments of the invention likewise relate to the isolated and/or purified polypeptides, characterized in that they comprise a polypeptide selected from at least one of the amino acid sequences of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 or one of their fragments.
Among the isolated and/or purified polypeptides, according to embodiments of the invention, are the isolated and/or purified polypeptides of amino acid sequence SEQ ID NOS:8-12, 25-29, 42-46, 59-63, 76-80, 93-97, 110-114, 127-131, 144-148, 161-165, 178-182, 195-199, 212-216, 229-233, 246-250, 263-267, 280-284, 297-301, 314-318, 331-335, 348-352, 365-369, 382-386, 399-403, 416-420, 433-437, 450-454, 467-471, 484-488, 501-505, 518-522, 535-539, 552-556, 569-573, 586-590, 603-607, 620-624, 637-641, 654-658, 671-675, 688-692, 705-709, 722-726, 739-743, 756-760, and 773-777, or fragments thereof or any other isolated and/or purified polypeptides that have a homology of at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7% identity with at least one of the sequences of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 or fragments thereof. As will be apparent to one of ordinary skill in the art, such homologues are easily created and identified using standard techniques and publicly available computer programs such as BLAST. As such, each homologue referenced above should be considered as set forth herein and fully described.
Embodiments of the invention also relate to the polypeptides, characterized in that they comprise a polypeptide selected from: a) a specific fragment of at least 5 amino acids of a polypeptide of an amino acid sequence according to the invention; b) a polypeptide homologous to a polypeptide such as defined in a); c) a specific biologically active fragment of a polypeptide such as defined in a) or b); and d) a polypeptide modified by a polypeptide such as defined in a), b) or c).
In the present description, the terms polypeptide, peptide and protein are interchangeable.
In embodiments of the invention, the isolated and/or purified polypeptides according to the invention may be glycosylated, pegylated, and/or otherwise post-translationally modified. In further embodiments, glycosylation, pegylation, and/or other post-translational modifications may occur in vivo or in vitro and/or may be performed using chemical techniques. In additional embodiments, any glycosylation, pegylation and/or other post-translational modifications may be N-linked or O-linked.
In embodiments of the invention, any one of the isolated and/or purified polypeptides according to the invention may be enzymatically or functionally active at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/or may be enzymatically or functionally active at a pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0. In further embodiments of the invention, glycosylation, pegylation, and/or other post-translational modification may be required for the isolated and/or purified polypeptides according to the invention to be enzymatically or functionally active at a pH at or below 8, 7, 6, 5, 4, 3, 2, 1, and/or 0 or at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius.
Aspects of the invention relate to polypeptides that are isolated or obtained by purification from natural sources, or else obtained by genetic recombination, or alternatively by chemical synthesis and that they may thus contain unnatural amino acids, as will be described below.
A “polypeptide fragment” according to the embodiments of the invention is understood as designating a polypeptide containing at least five (5) consecutive amino acids, preferably ten (10) consecutive amino acids or fifteen (15) consecutive amino acids.
In the present invention, a specific polypeptide fragment is understood as designating the consecutive polypeptide fragment coded for by a specific fragment nucleotide sequence according to the invention.
“Homologous polypeptide” will be understood as designating the polypeptides having, with respect to the natural polypeptide, certain modifications such as, in particular, a deletion, addition, or substitution of at least one amino acid, a truncation, a prolongation, a chimeric fusion, and/or a mutation. Among the homologous polypeptides, those are preferred whose amino acid sequence has at least 80% or 90%, homology with the sequences of amino acids of polypeptides according to the invention.
“Specific homologous polypeptide” will be understood as designating the homologous polypeptides such as defined above and having a specific fragment of polypeptide according to the invention.
In the case of a substitution, one or more consecutive or nonconsecutive amino acids are replaced by “equivalent” amino acids. The expression “equivalent” amino acid is directed here at designating any amino acid capable of being substituted by one of the amino acids of the base structure without, however, essentially modifying the biological activities of the corresponding peptides and such that they will be defined by the following. As will be apparent to one of ordinary skill in the art, such substitutions are easily created and identified using standard molecular biology techniques and publicly available computer programs such as BLAST. As such, each substitution referenced above should be considered as set forth herein and fully described. Examples of such substitutions in the amino acid sequences SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 may include those isolated and/or purified polypeptides of amino acid sequence SEQ ID NOS:8-12, 25-29, 42-46, 59-63, 76-80, 93-97, 110-114, 127-131, 144-148, 161-165, 178-182, 195-199, 212-216, 229-233, 246-250, 263-267, 280-284, 297-301, 314-318, 331-335, 348-352, 365-369, 382-386, 399-403, 416-420, 433-437, 450-454, 467-471, 484-488, 501-505, 518-522, 535-539, 552-556, 569-573, 586-590, 603-607, 620-624, 637-641, 654-658, 671-675, 688-692, 705-709, 722-726, 739-743, 756-760, and 773-777. These equivalent amino acids may be determined either by depending on their structural homology with the amino acids that they substitute, or on results of comparative tests of biological activity between the different polypeptides, which are capable of being carried out.
By way of non-limiting example, the possibilities of substitutions capable of being carried out without resulting in an extensive modification of the biological activity of the corresponding modified polypeptides will be mentioned, the replacement, for example, of leucine by valine or isoleucine, of aspartic acid by glutamic acid, of glutamine by asparagine, of arginine by lysine etc., the reverse substitutions naturally being envisageable under the same conditions.
In a further embodiment, substitutions are limited to substitutions in amino acids not conserved among other proteins that have similar identified enzymatic activity. For example, one of ordinary skill in the art may align proteins of the same function in similar organisms and determine which amino acids are generally conserved among proteins of that function. One example of a program that may be used to generate such alignments is available on the worldwide web at charite.de/bioinf/strap/ in conjunction with the databases provided by the NCBI. Examples of such polypeptides may include, but are not limited to, those found in amino acid sequence SEQ ID NOS:8-12, 25-29, 42-46, 59-63, 76-80, 93-97, 110-114, 127-131, 144-148, 161-165, 178-182, 195-199, 212-216, 229-233, 246-250, 263-267, 280-284, 297-301, 314-318, 331-335, 348-352, 365-369, 382-386, 399-403, 416-420, 433-437, 450-454, 467-471, 484-488, 501-505, 518-522, 535-539, 552-556, 569-573, 586-590, 603-607, 620-624, 637-641, 654-658, 671-675, 688-692, 705-709, 722-726, 739-743, 756-760, and 773-777.
Thus, according to one embodiment of the invention, substitutions or mutation may be made at positions that are generally conserved among proteins of that function. In a further embodiment, nucleic acid sequences may be mutated or substituted such that the amino acid they code for is unchanged (degenerate substitutions and/mutations) and/or mutated or substituted such that any resulting amino acid substitutions or mutation are made at positions that are generally conserved among proteins of that function. Examples of such nucleic acid sequences may include, but are not limited to, those found in are the nucleotide sequences of SEQ ID NOS:13-17, 30-34, 47-51, 64-68, 81-85, 98-102, 115-119, 132-136, 149-153, 166-170, 183-187, 200-204, 217-221, 234-238, 251-255, 268-272, 285-289, 302-306, 319-323, 336-340, 353-357, 370-374, 387-391, 404-408, 421-425, 438-442, 455-459, 472-476, 489-493, 506-510, 523-527, 540-544, 557-561, 574-578, 591-595, 608-612, 625-629, 642-646, 659-663, 676-680, 693-697, 710-714, 727-731, 744-748, 761-765, 778-782 or fragments thereof.
The specific homologous polypeptides likewise correspond to polypeptides coded for by the specific homologous nucleotide sequences such as defined above and thus comprise in the present definition the polypeptides, which are mutated or correspond to variants, which can exist in Alicyclobacillus acidocaldarius, and which especially correspond to truncations, substitutions, deletions, and/or additions of at least one amino acid residue.
“Specific biologically active fragment of a polypeptide” according to an embodiment of the invention will be understood in particular as designating a specific polypeptide fragment, such as defined above, having at least one of the characteristics of polypeptides according to the invention. In certain embodiments the peptide is capable of behaving as at least one of the types of proteins outlined in Table 1.
The polypeptide fragments according to embodiments of the invention can correspond to isolated or purified fragments naturally present in Alicyclobacillus acidocaldarius or correspond to fragments that can be obtained by cleavage of the polypeptide by a proteolytic enzyme, such as trypsin or chymotrypsin or collagenase, or by a chemical reagent, such as cyanogen bromide (CNBr). Such polypeptide fragments can likewise just as easily be prepared by chemical synthesis, from hosts transformed by an expression vector according to the invention containing a nucleic acid allowing the expression of the fragments, placed under the control of appropriate regulation and/or expression elements.
“Modified polypeptide” of a polypeptide according to an embodiment of the invention is understood as designating a polypeptide obtained by genetic recombination or by chemical synthesis as will be described below, having at least one modification with respect to the normal sequence. These modifications may or may not be able to bear on amino acids at the origin of specificity, and/or of activity, or at the origin of the structural conformation, localization, and of the capacity of membrane insertion of the polypeptide according to the invention. It will thus be possible to create polypeptides of equivalent, increased, or decreased activity, and of equivalent, narrower, or wider specificity. Among the modified polypeptides, it is necessary to mention the polypeptides in which up to five (5) or more amino acids can be modified, truncated at the N- or C-terminal end, or even deleted or added.
The methods allowing the modulations on eukaryotic or prokaryotic cells to be demonstrated are well known to the person of ordinary skill in the art. It is likewise well understood that it will be possible to use the nucleotide sequences coding for the modified polypeptides for the modulations, for example, through vectors according to the invention and described below.
The preceding modified polypeptides can be obtained by using combinatorial chemistry, in which it is possible to systematically vary parts of the polypeptide before testing them on models, cell cultures or microorganisms, for example, to select the compounds that are most active or have the properties sought.
Chemical synthesis likewise has the advantage of being able to use unnatural amino acids, or nonpeptide bonds.
Thus, in order to improve the duration of life of the polypeptides according to the invention, it may be of interest to use unnatural amino acids, for example in D faun, or else amino acid analogs, especially sulfur-containing forms, for example.
Finally, it will be possible to integrate the structure of the polypeptides according to the invention, its specific or modified homologous forms, into chemical structures of polypeptide type or others. Thus, it may be of interest to provide at the N- and C-terminal ends molecules not recognized by proteases.
The nucleotide sequences coding for a polypeptide according to the invention are likewise part of the invention.
The invention likewise relates to nucleotide sequences utilizable as a primer or probe, characterized in that the sequences are selected from the nucleotide sequences according to the invention.
It is well understood that the present invention, in various embodiments, likewise relates to specific polypeptides of Alicyclobacillus acidocaldarius, coded for by nucleotide sequences, capable of being obtained by purification from natural polypeptides, by genetic recombination or by chemical synthesis by procedures well known to a person skilled in the art and such as described in particular below. In the same manner, the labeled or unlabeled mono- or polyclonal antibodies directed against the specific polypeptides coded for by the nucleotide sequences are also encompassed by the invention.
Embodiments of the invention additionally relate to the use of a nucleotide sequence according to the invention as a primer or probe for the detection and/or the amplification of nucleic acid sequences.
The nucleotide sequences according to embodiments of the invention can thus be used to amplify nucleotide sequences, especially by the PCR (polymerase chain reaction) technique (Erlich, 1989; Innis et al., 1990; Rolfs et al., 1991; and White et al., 1997).
These oligodeoxyribonucleotide or oligoribonucleotide primers advantageously have a length of at least eight (8) nucleotides, preferably of at least twelve (12) nucleotides, and even more preferentially at least twenty (20) nucleotides.
Other amplification techniques of the target nucleic acid can be advantageously employed as alternatives to PCR.
The nucleotide sequences of the invention, in particular the primers according to the invention, can likewise be employed in other procedures of amplification of a target nucleic acid, such as: the TAS (Transcription-based Amplification System) technique, described by Kwoh et al. in 1989; the 3SR (Self-Sustained Sequence Replication) technique, described by Guatelli et al. in 1990; the NASBA (Nucleic Acid Sequence Based Amplification) technique, described by Kievits et al. in 1991; the SDA (Strand Displacement Amplification) technique (Walker et al., 1992); the TMA (Transcription Mediated Amplification) technique.
The polynucleotides of the invention can also be employed in techniques of amplification or of modification of the nucleic acid serving as a probe, such as: the LCR (Ligase Chain Reaction) technique, described by Landegren et al. in 1988 and improved by Barany et al. in 1991, which employs a thermostable ligase; the RCR (Repair Chain Reaction) technique, described by Segev in 1992; the CPR (Cycling Probe Reaction) technique, described by Duck et al. in 1990; the amplification technique with Q-beta replicase, described by Miele et al. in 1983 and especially improved by Chu et al. in 1986, Lizardi et al. in 1988, then by Burg et al., as well as by Stone et al. in 1996.
In the case where the target polynucleotide to be detected is possibly an RNA, for example an mRNA, it will be possible to use, prior to the employment of an amplification reaction with the aid of at least one primer according to the invention or to the employment of a detection procedure with the aid of at least one probe of the invention, an enzyme of reverse transcriptase type in order to obtain a cDNA from the RNA contained in the biological sample. The cDNA obtained will thus serve as a target for the primer(s) or the probe(s) employed in the amplification or detection procedure according to the invention.
The detection probe will be chosen in such a manner that it hybridizes with the target sequence or the amplicon generated from the target sequence. By way of sequence, such a probe will advantageously have a sequence of at least twelve (12) nucleotides, in particular of at least twenty (20) nucleotides, and preferably of at least one hundred (100) nucleotides.
Embodiments of the invention also comprise the nucleotide sequences utilizable as a probe or primer according to the invention, characterized in that they are labeled with a radioactive compound or with a nonradioactive compound.
The unlabeled nucleotide sequences can be used directly as probes or primers, although the sequences are generally labeled with a radioactive isotope (32P, 35S, 3H, 125I) or with a nonradioactive molecule (biotin, acetylaminofluorene, digoxigenin, 5-bromodeoxyuridine, fluorescein) to obtain probes that are utilizable for numerous applications.
Examples of nonradioactive labeling of nucleotide sequences are described, for example, in French Patent No. 7810975 or by Urdea et al. or by Sanchez-Pescador et al., both in 1988.
In the latter case, it will also be possible to use one of the labeling methods described in patents FR-2 422 956 and FR-2 518 755.
The hybridization technique can be carried out in various manners (Matthews et al., 1988). The most general method consists in immobilizing the nucleic acid extract of cells on a support (such as nitrocellulose, nylon, polystyrene) and in incubating, under well-defined conditions, the immobilized target nucleic acid with the probe. After hybridization, the excess of probe is eliminated and the hybrid molecules formed are detected by the appropriate method (measurement of the radioactivity, of the fluorescence or of the enzymatic activity linked to the probe).
The invention, in various embodiments, likewise comprises the nucleotide sequences according to the invention, characterized in that they are immobilized on a support, covalently or noncovalently.
According to another advantageous mode of employing nucleotide sequences according to the invention, the latter can be used immobilized on a support and can thus serve to capture, by specific hybridization, the target nucleic acid obtained from the biological sample to be tested. If necessary, the solid support is separated from the sample and the hybridization complex formed between the capture probe, and the target nucleic acid is then detected with the aid of a second probe, a so-called detection probe, labeled with an easily detectable element.
Another aspect of the present invention is a vector for the cloning and/or expression of a sequence, characterized in that it contains a nucleotide sequence according to the invention.
The vectors according to the invention, characterized in that they contain the elements allowing the integration, expression and/or the secretion of the nucleotide sequences in a determined host cell, are likewise part of the invention.
The vector may then contain a promoter, signals of initiation and termination of translation, as well as appropriate regions of regulation of transcription. It may be able to be maintained stably in the host cell and can optionally have particular signals specifying the secretion of the translated protein. These different elements may be chosen as a function of the host cell used. To this end, the nucleotide sequences according to the invention may be inserted into autonomous replication vectors within the chosen host, or integrated vectors of the chosen host.
Such vectors will be prepared according to the methods currently used by the person skilled in the art, and it will be possible to introduce the clones resulting therefrom into an appropriate host by standard methods, such as, for example, lipofection, electroporation, and thermal shock.
The vectors according to the invention are, for example, vectors of plasmid or viral origin. One example of a vector for the expression of polypeptides of the invention is baculovirus.
These vectors are useful for transforming host cells in order to clone or to express the nucleotide sequences of the invention.
The invention likewise comprises the host cells transformed by a vector according to the invention.
These cells can be obtained by the introduction into host cells of a nucleotide sequence inserted into a vector such as defined above, then the culturing of the cells under conditions allowing the replication and/or expression of the transfected nucleotide sequence.
The host cell can be selected from prokaryotic or eukaryotic systems, such as, for example, bacterial cells (Olins and Lee, 1993), but likewise yeast cells (Buckholz, 1993), as well as plants cells, such as Arabidopsis sp., and animal cells, in particular the cultures of mammalian cells (Edwards and Aruffo, 1993), for example, Chinese hamster ovary (CHO) cells, but likewise the cells of insects in which it is possible to use procedures employing baculoviruses, for example sf9 insect cells (Luckow, 1993).
Embodiments of the invention likewise relate to organisms comprising one of the transformed cells according to the invention.
The obtainment of transgenic organisms according to the invention expressing one or more of the genes of Alicyclobacillus acidocaldarius or part of the genes may be carried out in, for example, rats, mice, or rabbits according to methods well known to the person skilled in the art, such as by viral or nonviral transfections. It will be possible to obtain the transgenic organisms expressing one or more of the genes by transfection of multiple copies of the genes under the control of a strong promoter of ubiquitous nature, or selective for one type of tissue. It will likewise be possible to obtain the transgenic organisms by homologous recombination in embryonic cell strains, transfer of these cell strains to embryos, selection of the affected chimeras at the level of the reproductive lines, and growth of the chimeras.
The transformed cells as well as the transgenic organisms according to the invention are utilizable in procedures for preparation of recombinant polypeptides.
It is today possible to produce recombinant polypeptides in relatively large quantity by genetic engineering using the cells transformed by expression vectors according to the invention or using transgenic organisms according to the invention.
The procedures for preparation of a polypeptide of the invention in recombinant form, characterized in that they employ a vector and/or a cell transformed by a vector according to the invention and/or a transgenic organism comprising one of the transformed cells according to the invention are themselves comprised in the present invention.
As used herein, “transformation” and “transformed” relate to the introduction of nucleic acids into a cell, whether prokaryotic or eukaryotic. Further, “transformation” and “transformed,” as used herein, need not relate to growth control or growth deregulation.
Among the procedures for preparation of a polypeptide of the invention in recombinant form, the preparation procedures employing a vector, and/or a cell transformed by the vector and/or a transgenic organism comprising one of the transformed cells, containing a nucleotide sequence according to the invention coding for a polypeptide of Alicyclobacillus acidocaldarius. 
A variant, according to the invention, may consist of producing a recombinant polypeptide fused to a “carrier” protein (chimeric protein). The advantage of this system is that it may allow stabilization of and/or a decrease in the proteolysis of the recombinant product, an increase in the solubility in the course of renaturation in vitro and/or a simplification of the purification when the fusion partner has an affinity for a specific ligand.
More particularly, the invention relates to a procedure for preparation of a polypeptide of the invention comprising the following steps: a) culture of transformed cells under conditions allowing the expression of a recombinant polypeptide of nucleotide sequence according to the invention; b) if need be, recovery of the recombinant polypeptide.
When the procedure for preparation of a polypeptide of the invention employs a transgenic organism according to the invention, the recombinant polypeptide is then extracted from the organism.
The invention also relates to a polypeptide that is capable of being obtained by a procedure of the invention such as described previously.
The invention also comprises a procedure for preparation of a synthetic polypeptide, characterized in that it uses a sequence of amino acids of polypeptides according to the invention.
The invention likewise relates to a synthetic polypeptide obtained by a procedure according to the invention.
The polypeptides according to the invention can likewise be prepared by techniques that are conventional in the field of the synthesis of peptides. This synthesis can be carried out in homogeneous solution or in solid phase.
For example, recourse can be made to the technique of synthesis in homogeneous solution described by Houben-Weyl in 1974.
This method of synthesis consists in successively condensing, two by two, the successive amino acids in the order required, or in condensing amino acids and fragments formed previously and already containing several amino acids in the appropriate order, or alternatively several fragments previously prepared in this way, it being understood that it will be necessary to protect beforehand all the reactive functions carried by these amino acids or fragments, with the exception of amine functions of one and carboxyls of the other or vice versa, which must normally be involved in the formation of peptide bonds, especially after activation of the carboxyl function, according to the methods well known in the synthesis of peptides.
Recourse may also be made to the technique described by Merrifield.
To make a peptide chain according to the Merrifield procedure, recourse is made to a very porous polymeric resin, on which is immobilized the first C-terminal amino acid of the chain. This amino acid is immobilized on a resin through its carboxyl group and its amine function is protected. The amino acids, which are going to form the peptide chain, are thus immobilized, one after the other, on the amino group, which is deprotected beforehand each time, of the portion of the peptide chain already formed, and which is attached to the resin. When the whole of the desired peptide chain has been formed, the protective groups of the different amino acids forming the peptide chain are eliminated and the peptide is detached from the resin with the aid of an acid.
The invention additionally relates to hybrid polypeptides having at least one polypeptide according to the invention, and a sequence of a polypeptide capable of inducing an immune response in man or animals.
Advantageously, the antigenic determinant is such that it is capable of inducing a humoral and/or cellular response.
It will be possible for such a determinant to comprise a polypeptide according to the invention in glycosylated, pegylated, and/or otherwise post-translationally modified form used with a view to obtaining immunogenic compositions capable of inducing the synthesis of antibodies directed against multiple epitopes.
These hybrid molecules can be formed, in part, of a polypeptide carrier molecule or of fragments thereof according to the invention, associated with a possibly immunogenic part, in particular an epitope of the diphtheria toxin, the tetanus toxin, a surface antigen of the hepatitis B virus (patent FR 7921811), the VP1 antigen of the poliomyelitis virus or any other viral or bacterial toxin or antigen.
The procedures for synthesis of hybrid molecules encompass the methods used in genetic engineering for constructing hybrid nucleotide sequences coding for the polypeptide sequences sought. It will be possible, for example, to refer advantageously to the technique for obtainment of genes coding for fusion proteins described by Minton in 1984.
The hybrid nucleotide sequences coding for a hybrid polypeptide as well as the hybrid polypeptides according to the invention characterized in that they are recombinant polypeptides obtained by the expression of the hybrid nucleotide sequences are likewise part of the invention.
The invention likewise comprises the vectors characterized in that they contain one of the hybrid nucleotide sequences. The host cells transformed by the vectors, the transgenic organisms comprising one of the transformed cells as well as the procedures for preparation of recombinant polypeptides using the vectors, the transformed cells and/or the transgenic organisms are, of course, likewise part of the invention.
The polypeptides according to the invention, the antibodies according to the invention described below and the nucleotide sequences according to the invention can advantageously be employed in procedures for the detection and/or identification of Alicyclobacillus acidocaldarius, in a sample capable of containing them. These procedures, according to the specificity of the polypeptides, the antibodies and the nucleotide sequences according to the invention, which will be used, will in particular be able to detect and/or to identify Alicyclobacillus acidocaldarius. 
The polypeptides according to the invention can advantageously be employed in a procedure for the detection and/or the identification of Alicyclobacillus acidocaldarius in a sample capable of containing them, characterized in that it comprises the following steps: a) contacting of this sample with a polypeptide or one of its fragments according to the invention (under conditions allowing an immunological reaction between the polypeptide and the antibodies possibly present in the biological sample); b) demonstration of the antigen-antibody complexes possibly formed.
Any conventional procedure can be employed for carrying out such a detection of the antigen-antibody complexes possibly formed.
By way of example, a preferred method brings into play immunoenzymatic processes according to the ELISA technique, by immunofluorescence, or radioimmunological (RIA) processes or their equivalent.
Thus, the invention likewise relates to the polypeptides according to the invention, labeled with the aid of an adequate label, such as, of the enzymatic, fluorescent or radioactive type.
Such methods comprise, for example, the following steps: deposition of determined quantities of a polypeptide composition according to the invention in the wells of a microtiter plate, introduction into the wells of increasing dilutions of serum, or of a biological sample other than that defined previously, having to be analyzed, incubation of the microtiter plate, introduction into the wells of the microtiter plate of labeled antibodies directed against pig immunoglobulins, the labeling of these antibodies having been carried out with the aid of an enzyme selected from those which are capable of hydrolyzing a substrate by modifying the absorption of the radiation of the latter, at least at a determined wavelength, for example at 550 nm, detection, by comparison with a control test, of the quantity of hydrolyzed substrate.
The polypeptides according to the invention allow monoclonal or polyclonal antibodies to be prepared, which are characterized in that they specifically recognize the polypeptides according to the invention. It will advantageously be possible to prepare the monoclonal antibodies from hybridomas according to the technique described by Köhler and Milstein in 1975. It will be possible to prepare the polyclonal antibodies, for example, by immunization of an animal, in particular a mouse, with a polypeptide or a DNA, according to the invention, associated with an adjuvant of the immune response, and then purification of the specific antibodies contained in the serum of the immunized animals on an affinity column on which the polypeptide, which has served as an antigen, has previously been immobilized. The polyclonal antibodies according to the invention can also be prepared by purification, on an affinity column on which a polypeptide according to the invention has previously been immobilized, of the antibodies contained in the serum of an animal immunologically challenged by Alicyclobacillus acidocaldarius, or a polypeptide or fragment according to the invention.
The invention likewise relates to mono- or polyclonal antibodies or their fragments, or chimeric antibodies, characterized in that they are capable of specifically recognizing a polypeptide according to the invention.
It will likewise be possible for the antibodies of the invention to be labeled in the same manner as described previously for the nucleic probes of the invention, such as a labeling of enzymatic, fluorescent or radioactive type.
The invention is additionally directed at a procedure for the detection and/or identification of Alicyclobacillus acidocaldarius in a sample, characterized in that it comprises the following steps: a) contacting of the sample with a mono or polyclonal antibody according to the invention (under conditions allowing an immunological reaction between the antibodies and the polypeptides of Alicyclobacillus acidocaldarius possibly present in the biological sample); b) demonstration of the antigen-antibody complex possibly formed.
The present invention likewise relates to a procedure for the detection and/or the identification of Alicyclobacillus acidocaldarius in a sample, characterized in that it employs a nucleotide sequence according to the invention.
More particularly, the invention relates to a procedure for the detection and/or the identification of Alicyclobacillus acidocaldarius in a sample, characterized in that it contains the following steps: a) if need be, isolation of the DNA from the sample to be analyzed; b) specific amplification of the DNA of the sample with the aid of at least one primer, or a pair of primers, according to the invention; c) demonstration of the amplification products.
These can be detected, for example, by the technique of molecular hybridization utilizing a nucleic probe according to the invention. This probe will advantageously be labeled with a nonradioactive (cold probe) or radioactive isotope.
For the purposes of the present invention, “DNA of the biological sample” or “DNA contained in the biological sample” will be understood as meaning either the DNA present in the biological sample considered, or possibly the cDNA obtained after the action of an enzyme of reverse transcriptase type on the RNA present in the biological sample.
A further embodiment of the invention comprises a method, characterized in that it comprises the following steps: a) contacting of a nucleotide probe according to the invention with a biological sample, the DNA contained in the biological sample having, if need be, previously been made accessible to hybridization under conditions allowing the hybridization of the probe with the DNA of the sample; b) demonstration of the hybrid formed between the nucleotide probe and the DNA of the biological sample.
The present invention also relates to a procedure according to the invention, characterized in that it comprises the following steps: a) contacting of a nucleotide probe immobilized on a support according to the invention with a biological sample, the DNA of the sample having, if need be, previously been made accessible to hybridization, under conditions allowing the hybridization of the probe with the DNA of the sample; b) contacting of the hybrid formed between the nucleotide probe immobilized on a support and the DNA contained in the biological sample, if need be after elimination of the DNA of the biological sample, which has not hybridized with the probe, with a nucleotide probe labeled according to the invention; c) demonstration of the novel hybrid formed in step b).
According to an advantageous embodiment of the procedure for detection and/or identification defined previously, this is characterized in that, prior to step a), the DNA of the biological sample is first amplified with the aid of at least one primer according to the invention.
Embodiments of methods include providing a recombinant, purified, and/or isolated polypeptide selected from the group consisting of a polypeptide having at least 90% sequence identity to SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 in or association with a cell membrane and transporting a sugar across the cell membrane using the a recombinant, purified, and/or isolated polypeptide in association with other cellular components.
Further embodiments of methods include placing a cell producing or encoding a recombinant, purified, and/or isolated nucleotide sequence comprising a nucleotide sequence selected from the group consisting of nucleotide sequences having at least 90% sequence identity to at least one of the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 and/or a recombinant, purified, and/or isolated polypeptide selected from the group consisting of a polypeptide having at least 90% sequence identity to at least one of the sequences of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 in a environment comprising temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/or a pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0.
The present invention provides cells that have been genetically manipulated to have an altered capacity to produce expressed proteins. In particular, the present invention relates to Gram-positive microorganisms, such as Bacillus species having enhanced expression of a protein of interest, wherein one or more chromosomal genes have been inactivated, and/or wherein one or more chromosomal genes have been deleted from the Bacillus chromosome. In some further embodiments, one or more indigenous chromosomal regions have been deleted from a corresponding wild-type Bacillus host chromosome. In further embodiments, the Bacillus is an Alicyclobacillus sp. or Alicyclobacillus acidocaldarius. 
In additional embodiments, methods of transporting sugars at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/or at a pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0 via a recombinant, purified, and/or isolated nucleotide sequence comprising a nucleotide sequence selected from the group consisting of nucleotide sequences having at least 90% sequence identity to at least one of the sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 and/or a recombinant, purified, and/or isolated polypeptide selected from the group consisting of a polypeptide having at least 90% sequence identity to at least one of the sequences of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766.
In embodiments of the invention, any one of the isolated and/or purified polypeptides, according to the invention, may be enzymatically or functionally active at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/or may be enzymatically or functionally active at a pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0. In further embodiments of the invention, glycosylation, pegylation, and/or other post-translational modification may be required for the isolated and/or purified polypeptides according to the invention to be enzymatically or functionally active at a pH at or below 8, 7, 6, 5, 4, 3, 2, 1, and/or 0 or at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius.
The invention is described in additional detail in the following illustrative examples. Although the examples may represent only selected embodiments of the invention, it should be understood that the following examples are illustrative and not limiting.
EXAMPLES
Example 1
Sugar Transport Using Nucleotide and Amino Acid Sequences from Alicyclobacillus acidocaldarius
Provided in SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 are nucleotide sequences isolated from Alicyclobacillus acidocaldarius and coding for the polypeptides of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766, respectively. The nucleotide sequences of SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 are placed into expression vectors using techniques standard in the art. The vectors are then provided to cells such as bacteria cells or eukaryotic cells such as Sf9 cells or CHO cells. In conjunction with the normal machinery present in the cells, the vectors comprising SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, and 767 produce the polypeptides of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766. The polypeptides of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 are then isolated and/or purified. The isolated and/or purified polypeptides of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 are then each demonstrated to have one or more of the activities provided in Table 1.
The isolated and/or purified polypeptides of SEQ ID NOS:1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, and 766 are placed or transported into a cellular membrane and are demonstrated to have activity in transporting sugars across the membrane in conjunction with other proteins or cellular components.
All references, including publications, patents, and patent applications, cited herein are hereby incorporated by reference to the same extent, as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
While this invention has been described in certain embodiments, the present invention can be further modified within the spirit and scope of this disclosure. This application is therefore intended to cover any variations, uses, or adaptations of the invention using its general principles. Further, this application is intended to cover such departures from the present disclosure as come within known or customary practice in the art to which this invention pertains and which fall within the limits of the appended claims and their legal equivalents.
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## Claims

1. An isolated nucleic acid comprising a nucleic acid sequence encoding a polypeptide having at least 90% sequence identity to SEQ ID No: 137, wherein the polypeptide has Na+/melibiose symporter activity.

2. The isolated nucleic acid of claim 1, wherein the polypeptide has activity at about pH 8.

3. The isolated nucleic acid of claim 1, wherein the polypeptide has activity at a temperature at about 35 degrees Celsius.

4. The isolated nucleic acid of claim 1, wherein the nucleic acid is present in a vector.

5. The isolated nucleic acid of claim 1, wherein the encoded polypeptide has activity below pH 8.

6. The isolated nucleic acid of claim 1, wherein the encoded polypeptide has activity at a temperature above 35 degrees Celsius.

7. The isolated nucleic acid according to claim 1, wherein said nucleic acid is as set forth in SEQ ID NO:138.

8. A method of transporting a sugar across a cell membrane, the method comprising:
providing to a cell the isolated nucleic acid of claim 1;
incorporating into or associating with the cell membrane of the cell the protein encoded by the nucleic acid; and
transporting a sugar across said cell membrane utilizing the protein encoded by the nucleic acid.

9. The method according to claim 8, wherein transporting a sugar across said cell membrane utilizing the protein encoded by the nucleic acid occurs at about pH 8.

10. The method according to claim 8, wherein transporting a sugar across said cell membrane utilizing the protein encoded by the nucleic acid occurs at a temperature at about 35 degrees Celsius.

11. The method according to claim 8, wherein moving a sugar across said cell membrane utilizing the protein encoded by the nucleic acid occurs below pH 8.

12. The method according to claim 8, wherein moving a sugar across said cell membrane utilizing the protein encoded by the nucleic acid occurs at a temperature above 35 degrees Celsius.