# Patent

## Title
Enhanced processive cellulases

## Abstract

Nucleic acid sequences encoding chimeric polypeptides that exhibit enhanced cellulase activities are disclosed herein. These nucleic acids may be expressed in hosts such as fungi, which in turn may be cultured to produce chimeric polypeptides. Also disclosed are chimeric polypeptides and their use in the degradation of cellulosic materials.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Application No. 61/576,585, filed Dec. 16, 2011, the contents of which are incorporated by reference in their entirety.


CONTRACTUAL ORIGIN
The United States Government has rights in this invention under Contract No. DE-AC36-08G028308 between the United States Department of Energy and Alliance for Sustainable Energy, LLC, the Manager and Operator of the National Renewable Energy Laboratory.


REFERENCE TO SEQUENCE LISTING
This application contains a Sequence Listing submitted as an electronic text file entitled “11-07_Seq_ST25.txt,” having a size in bytes of 96 kb and created on Dec. 14, 2012. Pursuant to 37 CFR §1.52(e)(5), the information contained in the above electronic file is hereby incorporated by reference in its entirety.
BACKGROUND
The production of sustainable transportation fuels and commodity chemicals from lignocellulosic biomass is a major component of the international renewable energy technology portfolio, which will ultimately provide significant energy, economic, and climate security for the world. However, plant cell walls are highly evolved heterogeneous composite structures, which represent a significant challenge to deconstruct selectively. The majority of the sugars locked in plant cell walls are from cellulose and hemicellulose, with the former being more recalcitrant to deconstruction.
To date, many processes have been developed to produce fuels from biomass-derived sugars, ranging from ethanol via fermentation to higher alcohols from genetically-modified organisms to hydrocarbons produced biologically or catalytically. Thus, over a wide range of fuel production options, there is significant impetus to develop cost-effective methods to produce sugars for upgrading to fuels and commodity chemicals. The current leading industrial option to produce sugars from lignocellulosic biomass utilizes a thermochemical pretreatment step that renders the plant cell wall more amenable to the effective application of enzyme cocktails that deconstruct cellulose and hemicellulose to soluble sugars. The enzymatic hydrolysis step alone represents a significant fraction of the operating and capital cost of lignocellulosic biofuel production. Most enzyme cocktails under development today are based on fungal or bacterial cellulase secretomes. The industrial emphasis on fungal cocktails originated from the United States Army's isolation of the fungus Trichoderma reesei (anamorph of Hypocrea jecorina) in the South Pacific in the late 1940s, which has grown into an important platform for the production of cellulases at extremely high protein titers. The use of bacterial cellulase cocktails has focused effort on both free cellulase systems and complexed enzyme (i.e., cellulosomal) systems, as well as engineering of cellulase-producing bacteria and fungi to produce fuels and chemicals directly in a process known as Consolidated Bioprocessing. In the fungal enzyme cocktails, the processive cellulases are the primary components, and provide the majority of the hydrolytic activity for cellulose conversion to glucose. The processive cellulases have thus been the focus of many structural and biochemical studies and the primary targets for cellulase engineering.
The foregoing examples of the related art and limitations related therewith are intended to be illustrative and not exclusive. Other limitations of the related art will become apparent to those of skill in the art upon a reading of the specification and a study of the drawings.
SUMMARY
The following embodiments and aspects thereof are described and illustrated in conjunction with systems, tools and methods that are meant to be exemplary and illustrative, not limiting in scope. In various embodiments, one or more of the above-described problems have been reduced or eliminated, while other embodiments are directed to other improvements.
Exemplary embodiments provide isolated nucleic acid molecules that encode chimeric Ce17A polypeptides that have cellulase activities at least 1.5-fold greater than wild-type Ce17A polypeptides. In certain embodiments, the chimeric Ce17A polypeptides comprise domains from Penicillium funiculosum and Trichoderma reesei Ce17A polypeptides, such as the catalytic domain (CD) from the Penicillium funiculosum Ce17A polypeptide and the carbohydrate-binding module (CBM) and linker domain from the Trichoderma reesei Ce17A polypeptide.
Additional embodiments provide chimeric Ce17A polypeptides that have cellulase activities at least 1.5-fold greater than wild-type Ce17A polypeptides and methods for degrading cellulose or lignocellulosic biomass by contacting a cellulose containing material with the isolated chimeric Ce17A polypeptides.
In addition to the exemplary aspects and embodiments described above, further aspects and embodiments will become apparent by reference to the drawings and by study of the following descriptions.



BRIEF DESCRIPTION OF THE DRAWINGS
Exemplary embodiments are illustrated in referenced figures of the drawings. It is intended that the embodiments and figures disclosed herein are to be considered illustrative rather than limiting.
FIG. 1 illustrates the Family 7 cellobiohydrolase (Ce17A) from T. reesei in the catalytically-active complex on a cellulose microfibril.
FIG. 2 shows the nucleic acid (SEQ ID NO:1) and amino acid (SEQ ID NO:2) sequences for wild-type Ce17A from Penicillium funiculosum. The linker domain is underlined and the CBM is in bold.
FIG. 3 shows the nucleic acid (SEQ ID NO:3) and amino acid (SEQ ID NO:4) sequences for wild-type Ce17A from Trichoderma reesei. The linker domain is underlined and the CBM is in bold.
FIG. 4 shows the nucleic acid (SEQ ID NO:5) and amino acid (SEQ ID NO:6) sequences for a chimeric Ce17A containing the CBM from Trichoderma reesei and the linker domain and catalytic domain from Penicillium funiculosum. The linker domain is underlined and the CBM is in bold.
FIG. 5 shows the nucleic acid (SEQ ID NO:7) and amino acid (SEQ ID NO:8) sequences for a chimeric Ce17A containing the CBM and linker domain from Trichoderma reesei and the catalytic domain from Penicillium funiculosum. The linker domain is underlined and the CBM is in bold.
FIG. 6 shows the nucleic acid (SEQ ID NO:9) and amino acid (SEQ ID NO:10) sequences for a chimeric Ce17A containing the CBM and catalytic domain from Trichoderma reesei and the linker domain from Penicillium funiculosum. The linker domain is underlined and the CBM is in bold.
FIG. 7 shows the nucleic acid (SEQ ID NO:11) and amino acid (SEQ ID NO:12) sequences for a chimeric Ce17A containing the CBM from Penicillium funiculosum and the catalytic domain and linker domain from Trichoderma reesei. The linker domain is underlined and the CBM is in bold.
FIG. 8 shows the nucleic acid (SEQ ID NO:13) and amino acid (SEQ ID NO:14) sequences for a chimeric Ce17A containing the CBM and linker domain from Penicillium funiculosum and the catalytic domain from Trichoderma reesei. The linker domain is underlined and the CBM is in bold.
FIG. 9 shows the nucleic acid (SEQ ID NO:15) and amino acid (SEQ ID NO:16) sequences for a chimeric Ce17A containing the CBM and catalytic domain from Penicillium funiculosum and the linker domain from Trichoderma reesei. The linker domain is underlined and the CBM is in bold.
FIG. 10 shows a diagram of plasmid pTr50 for expression of chimeric genes in T. reesei strain AST1116. The gene of interest can be added by digesting the plasmid and the insert with NdeI and XbaI. The vector may then linearized by digesting with XhoI.
FIG. 11 shows an interpolation to determine equivalence of TTP chimera to 46.68 mg/g cellulose wild-type T. reesei Ce17A at about 80% conversion using 27-hour digestion data.
FIG. 12 shows conversion of dilute-acid pretreated corn stover as a function of time. The chimeras are listed as shown in Table 3 in the order of CBM-Linker-Catalytic Domain. T=T. reesei and P=P. funiculosum. 
FIG. 13 illustrates additional activity data for the TTP chimera.
FIG. 14 illustrates a comparison of the time required for the T-T-P chimera and wild-type T. reesei Ce17A to reach 80% conversion of pretreated corn stover cellulose at equal enzyme loadings.
FIG. 15 compares the amount of time to reach 80% conversion of pretreated corn stover cellulose for the wild-type T. reesei Ce17A (46 mg/g cellulose) and the T-T-P chimera at various enzyme loadings (24, 18, 12, 9 and 6 mg/g cellulose).
FIG. 16 illustrates a comparison of the time required for the T-T-P chimera (▪), P-T-P chimera (*), natively expressed wild-type P. funiculosum Ce17A (Pfun WT; ▴) and wild-type P. funiculosum Ce17A expressed in T. reesei (P-P-P; ×) to reach 80% conversion of cellulose at equal enzyme loadings.



DETAILED DESCRIPTION
Nucleic acid molecules encoding chimeric Ce17A polypeptides that function as improved cellulases are disclosed herein. These nucleic acids may be expressed in hosts such as fungi, which in turn may be cultured to produce cellulases. Also disclosed are methods of using chimeric Ce17A polypeptides for the conversion of cellulose to sugars such as glucose.
Despite efforts to engineer processive cellulases with significantly improved activities, few successes have been demonstrated. The results of past efforts have been summarized, for example, in a review article by Wilson (Curr. Opin. Biotechnol. 20:295-299 (2009) (noting that “[a]t this time there are no published reports of engineered cellulases with major (greater than 1.5-fold) increases in activity on crystalline cellulose.”). Prior cellulase engineering has focused upon screening small sets of rationally guided mutations for higher thermal stability and subsequent modest gains in activity at higher conversion temperatures. Significant activity improvement in processive cellulase enzymes on realistic substrates at industrially relevant enzyme loadings and substrate conversion levels remains to be demonstrated.
Disclosed herein are methods for dramatically improving the activity of processive cellulases (e.g., the Glycoside Hydrolase Family 7 cellobiohydrolase (Ce17A)) by exchanging domains from Family 7 cellulases. The resulting chimeric Ce17A polypeptides surprisingly exhibit up to, or in excess of, 3-fold cellulase activity improvement when compared with the wild-type Ce17A polypeptides from which they were derived.
Family 7 cellobiohydrolases are expressed by fungi and are typically comprised of three sub-domains: a small Family 1 carbohydrate-binding module (CBM) connected to a large catalytic domain (CD) by a flexible linker peptide. FIG. 1 shows the catalytically-active complex of Ce17A from T. reesei. One or more processive Glycoside Hydrolase Family 7 cellobiohydrolases (e.g., Ce17A) typically comprise up to 70% by mass of fungal enzyme cocktails used to convert cellulosic materials to component sugars for subsequent fermentation to, for example, biofuels such as ethanol.
Rational engineering of cellobiohydrolases requires insight into the structure and function of the individual sub-domains, as well as the entire enzyme complexed with cellulose. Such insights are becoming possible with the advent of advanced experimental and computational techniques. Hypotheses as to the role of the individual sub-domains have remained relatively unchanged since the first structural studies of multi-domain cellulases.
The CBM is thought to be primarily responsible for increasing the binding affinity of a given cellulase CD to a cellulose substrate, thus ensuring a high catalyst concentration at the solid surface. The linker peptide/domain is thought to act as a flexible tether between the CBM and CD, but has no verified function beyond connecting these two domains. It is still unknown if the linker interacts with cellulose or aids in CBM binding. The CD in processive Family 7 cellulases exhibits a long tunnel for threading a single polymer chain of cellulose for complexation and hydrolysis to the disaccharide cellobiose. The putative catalytic cycle of Ce17A includes surface binding, locating a free cellulose chain end, chain complexation, hydrolysis, product expulsion, and processivity until the cellulase consumes an entire chain or becomes stuck due to obstacles in its path.
As used herein, the terms “chimeric polypeptide” or “chimera” refer to a polypeptide composed of parts of different wild-type polypeptides and typically composed of discrete functional domains from different polypeptides. For example, a chimeric Ce17A polypeptide may comprise a CD, linker domain, or CBM from two or more distinct Ce17A polypeptides. For exemplary purposes, the present disclosure is directed to chimeric polypeptides comprising domains from the Ce17A polypeptides of Penicillium funiculosum and Trichoderma reesei. However, the concepts disclosed herein encompass chimeras of Ce17A polypeptides from other filamentous fungi that exhibit enhanced enzymatic activities. The amino acid sequences for the wild-type Penicillium funiculosum (SEQ ID NO:2) and Trichoderma reesei (SEQ ID NO:4) Ce17A polypeptides and the CD, linker and CBM of each are illustrated in FIGS. 2 and 3, respectively.
Examples of chimeric Ce17A polypeptides include those set forth in Table 1 below, wherein T represents the indicated Ce17A polypeptide domain from T. reesei and P represents the indicated Ce17A polypeptide domain from P. funiculosum.












TABLE 1





CBM
Linker
CD
FIG.
Nucleic Acid
Amino Acid







T
P
P
4
SEQ ID NO: 5
SEQ ID NO: 6


T
T
P
5
SEQ ID NO: 7
SEQ ID NO: 8


T
P
T
6
SEQ ID NO: 9
SEQ ID NO: 10


P
T
T
7
SEQ ID NO: 11
SEQ ID NO: 12


P
P
T
8
SEQ ID NO: 13
SEQ ID NO: 14


P
T
P
9
SEQ ID NO: 15
SEQ ID NO: 16









Chimeras may also include CBMs, linker domains, and CDs from other Ce17A polypeptides, including Ce17A polypeptides from Humicola insolens, Aspergillus niger, Chrysosporium lucknowense, Fusarium oxysporum, Hypocrea koningii, Malanocarpus albomyces, Neurospora crassa, Phanerochaete chrysosporium, and Thielavia terristris. 
The chimeric Ce17A polypeptides exhibit surprisingly improved cellulase activities when compared to the wild-type Ce17A polypeptides from which they were derived. In some embodiments, the reference wild-type Ce17A polypeptide may be the source of the CD, the source of the linker domain, or the source of the CBM. For example, activity of the TTP chimera (CBM-linker-CD) may be relative to the activity of the wild-type Ce17A polypeptide from Trichoderma reesei or Penicillium funiculosum. 
The term “improved cellulase activity” refers to an increased rate of hydrolysis of a cellulosic substrate. Relative activities for chimeric and wild-type Ce17A polypeptides can be determined using conventional assays, including those discussed in the Examples below. Additional assays suitable for determining cellulase activity include hydrolysis assays on industrially relevant cellulose-containing substrates such as pretreated corn stover. Hydrolysis assays on crystalline cellulose or amorphous cellulose or on small molecule fluorescent reporters may also be used to determine cellulase activity. In certain embodiments, cellulase activity is expressed as the amount of time or enzyme concentration needed to reach a certain percentage (e.g., 80%) of cellulose conversion to sugars.
In contrast to the results of previous attempts to engineer processive cellulases, the chimeric Ce17A polypeptides herein exhibit cellulase activities that are at least 1.5-fold greater than the wild-type Ce17A polypeptide and that can reach at least 3-fold greater activity. In certain embodiments, the chimeric Ce17A polypeptides exhibit cellulase activities that are at least 1.1-, 1.2-, 1.3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2-, 2.1-, 2.2-, 2.3-, 2.4-, 2.5-, 2.6-, 2.7-, 2.8-, 2.9-, 3-, 3.1-, 3.2-, 3.3-, 3.4-, 3.5, 3.6-, 3.7-, 3.8-, 3.9-, 4-, 4.1-, 4.2-, 4.3-, 4.4-, 4.5, 4.6-, 4.7-, 4.8-, 4.9-, or 5-fold greater than the wild-type Ce17A polypeptide.
“Nucleic acid” or “polynucleotide” as used herein refers to purine- and pyrimidine-containing polymers of any length, either polyribonucleotides or polydeoxyribonucleotide or mixed polyribo-polydeoxyribonucleotides. This includes single- and double-stranded molecules (i.e., DNA-DNA, DNA-RNA and RNA-RNA hybrids) as well as “protein nucleic acids” (PNA) formed by conjugating bases to an amino acid backbone. This also includes nucleic acids containing modified bases.
Nucleic acids referred to herein as “isolated” are nucleic acids that have been removed from their natural milieu or separated away from the nucleic acids of the genomic DNA or cellular RNA of their source of origin (e.g., as it exists in cells or in a mixture of nucleic acids such as a library), and may have undergone further processing. Isolated nucleic acids include nucleic acids obtained by methods described herein, similar methods or other suitable methods, including essentially pure nucleic acids, nucleic acids produced by chemical synthesis, by combinations of biological and chemical methods, and recombinant nucleic acids that are isolated.
Nucleic acids referred to herein as “recombinant” are nucleic acids which have been produced by recombinant DNA methodology, including those nucleic acids that are generated by procedures that rely upon a method of artificial replication, such as the polymerase chain reaction (PCR) and/or cloning into a vector using restriction enzymes. Recombinant nucleic acids also include those that result from recombination events that occur through the natural mechanisms of cells, but are selected for after the introduction to the cells of nucleic acids designed to allow or make probable a desired recombination event. Portions of isolated nucleic acids that code for polypeptides having a certain function can be identified and isolated by, for example, the method disclosed in U.S. Pat. No. 4,952,501.
An isolated nucleic acid molecule can be isolated from its natural source or produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning) or chemical synthesis. Isolated nucleic acid molecules can include, for example, genes, natural allelic variants of genes, coding regions or portions thereof, and coding and/or regulatory regions modified by nucleotide insertions, deletions, substitutions, and/or inversions in a manner such that the modifications do not substantially interfere with the nucleic acid molecule's ability to encode a polypeptide or to form stable hybrids under stringent conditions with natural gene isolates. An isolated nucleic acid molecule can include degeneracies. As used herein, nucleotide degeneracy refers to the phenomenon that one amino acid can be encoded by different nucleotide codons. Thus, the nucleic acid sequence of a nucleic acid molecule that encodes a protein or polypeptide can vary due to degeneracies.
Unless so specified, a nucleic acid molecule is not required to encode a protein having protein activity. A nucleic acid molecule can encode a truncated, mutated or inactive protein, for example. In addition, nucleic acid molecules may also be useful as probes and primers for the identification, isolation and/or purification of other nucleic acid molecules, independent of a protein-encoding function.
Suitable nucleic acids include fragments or variants (e.g., of SEQ ID NO: 5, 7, 9, 11, 13 or 15) that encode a functional cellulase. For example, a fragment can comprise the minimum nucleotides required to encode a functional cellulase. Nucleic acid variants include nucleic acids with one or more nucleotide additions, deletions, substitutions, including transitions and transversions, insertion, or modifications (e.g., via RNA or DNA analogs). Alterations may occur at the 5′ or 3′ terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
In certain embodiments, a nucleic acid may be identical to the sequence represented as SEQ ID NO: 5, 7, 9, 11, 13 or 15. In other embodiments, the nucleic acids may be least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 5, 7, 9, 11, 13 or 15, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 5, 7, 9, 11, 13 or 15. Sequence identity calculations can be performed using computer programs, hybridization methods, or calculations. Exemplary computer program methods to determine identity and similarity between two sequences include, but are not limited to, the GCG program package, BLASTN, BLASTX, TBLASTX, and FASTA. The BLAST programs are publicly available from NCBI and other sources. For example, nucleotide sequence identity can be determined by comparing query sequences to sequences in publicly available sequence databases (NCBI) using the BLASTN2 algorithm.
Embodiments of the nucleic acids include those that encode a chimeric Ce17A polypeptide that functions as a cellulase or functional equivalents thereof. The amino acid sequences of exemplary chimeric Ce17A polypeptides are depicted in FIGS. 4-9 and represented by SEQ ID NOS:6, 8, 10, 12, 14 and 16. A functional equivalent includes fragments or variants of these that exhibit the ability to function as a cellulase. As a result of the degeneracy of the genetic code, many nucleic acid sequences can encode a polypeptide having, for example, the amino acid sequence of SEQ ID NO:6, 8, 10, 12, 14 or 16. Such functionally equivalent variants are contemplated herein.
Altered or variant nucleic acids can be produced by one of skill in the art using the sequence data illustrated herein and standard techniques known in the art. Variant nucleic acids may be detected and isolated by hybridization under high stringency conditions or moderate stringency conditions, for example, which are chosen to prevent hybridization of nucleic acids having non-complementary sequences. “Stringency conditions” for hybridizations is a term of art that refers to the conditions of temperature and buffer concentration that permit hybridization of a particular nucleic acid to another nucleic acid in which the first nucleic acid may be perfectly complementary to the second, or the first and second may share some degree of complementarity that is less than perfect.
Nucleic acids may be derived from a variety of sources including DNA, cDNA, synthetic DNA, synthetic RNA, or combinations thereof. Such sequences may comprise genomic DNA, which may or may not include naturally occurring introns. Moreover, such genomic DNA may be obtained in association with promoter regions or poly (A) sequences. The sequences, genomic DNA, or cDNA may be obtained in any of several ways. Genomic DNA can be extracted and purified from suitable cells by means well known in the art. Alternatively, mRNA can be isolated from a cell and used to produce cDNA by reverse transcription or other means.
Oligonucleotides that are fragments of SEQ ID NO: 5, 7, 9, 11, 13 or 15 and antisense nucleic acids that are complementary, in whole or in part, to SEQ ID NO: 5, 7, 9, 11, 13 or 15 are contemplated herein. Oligonucleotides may be used as primers or probes or for any other use known in the art. Antisense nucleic acids may be used, for example, to inhibit gene expression when introduced into a cell or for any other use known in the art. Oligonucleotides and antisense nucleic acids can be produced by standard techniques known in the art.
Also disclosed herein are recombinant vectors, including expression vectors, containing nucleic acids encoding chimeric Ce17A polypeptides. A “recombinant vector” is a nucleic acid molecule that is used as a tool for manipulating a nucleic acid sequence of choice or for introducing such a nucleic acid sequence into a host cell. A recombinant vector may be suitable for use in cloning, sequencing, or otherwise manipulating the nucleic acid sequence of choice, such as by expressing or delivering the nucleic acid sequence of choice into a host cell to form a recombinant cell. Such a vector typically contains heterologous nucleic acid sequences not naturally found adjacent to a nucleic acid sequence of choice, although the vector can also contain regulatory nucleic acid sequences (e.g., promoters, untranslated regions) that are naturally found adjacent to the nucleic acid sequences of choice or that are useful for expression of the nucleic acid molecules.
A recombinant vector can be either RNA or DNA, either prokaryotic or eukaryotic, and typically is a plasmid. The vector can be maintained as an extrachromosomal element (e.g., a plasmid) or it can be integrated into the chromosome of a recombinant host cell. The entire vector can remain in place within a host cell, or under certain conditions, the plasmid DNA can be deleted, leaving behind the nucleic acid molecule of choice. An integrated nucleic acid molecule can be under chromosomal promoter control, under native or plasmid promoter control, or under a combination of several promoter controls. Single or multiple copies of the nucleic acid molecule can be integrated into the chromosome. A recombinant vector can contain at least one selectable marker.
The term “expression vector” refers to a recombinant vector that is capable of directing the expression of a nucleic acid sequence that has been cloned into it after insertion into a host cell or other (e.g., cell-free) expression system. A nucleic acid sequence is “expressed” when it is transcribed to yield an mRNA sequence. In most cases, this transcript will be translated to yield an amino acid sequence. The cloned gene is usually placed under the control of (i.e., operably linked to) an expression control sequence. The phrase “operatively linked” refers to linking a nucleic acid molecule to an expression control sequence in a manner such that the molecule can be expressed when introduced (i.e., transformed, transduced, transfected, conjugated or conduced) into a host cell.
Recombinant vectors and expression vectors may contain one or more regulatory sequences or expression control sequences. Regulatory sequences broadly encompass expression control sequences (e.g., transcription control sequences or translation control sequences), as well as sequences that allow for vector replication in a host cell. Transcription control sequences are sequences that control the initiation, elongation, or termination of transcription. Suitable regulatory sequences include any sequence that can function in a host cell or organism into which the recombinant nucleic acid molecule is to be introduced, including those that control transcription initiation, such as promoter, enhancer, terminator, operator and repressor sequences. Additional regulatory sequences include translation regulatory sequences, origins of replication, and other regulatory sequences that are compatible with the recombinant cell. The expression vectors may contain elements that allow for constitutive expression or inducible expression of the protein or proteins of interest. Numerous inducible and constitutive expression systems are known in the art.
Typically, an expression vector includes at least one nucleic acid molecule encoding a chimeric Ce17A polypeptide operatively linked to one or more expression control sequences (e.g., transcription control sequences or translation control sequences). In one aspect, an expression vector may comprise a nucleic acid encoding a chimeric Ce17A polypeptide, as described herein, operably linked to at least one regulatory sequence. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of polypeptide to be expressed.
Expression and recombinant vectors may contain a selectable marker, a gene encoding a protein necessary for survival or growth of a host cell transformed with the vector. The presence of this gene allows growth of only those host cells that express the vector when grown in the appropriate selective media. Typical selection genes encode proteins that confer resistance to antibiotics or other toxic substances, complement auxotrophic deficiencies, or supply critical nutrients not available from a particular media. Markers may be an inducible or non-inducible gene and will generally allow for positive selection. Non-limiting examples of selectable markers include the ampicillin resistance marker (i.e., beta-lactamase), tetracycline resistance marker, neomycin/kanamycin resistance marker (i.e., neomycin phosphotransferase), dihydrofolate reductase, glutamine synthetase, and the like. The choice of the proper selectable marker will depend on the host cell, and appropriate markers for different hosts as understood by those of skill in the art.
Suitable expression vectors may include (or may be derived from) plasmid vectors that are well known in the art, such as those commonly available from commercial sources. The Examples below illustrate the construction of exemplary expression vectors containing chimeric Ce17A polypeptides. Vectors can contain one or more replication and inheritance systems for cloning or expression, one or more markers for selection in the host, and one or more expression cassettes. The inserted coding sequences can be synthesized by standard methods, isolated from natural sources, or prepared as hybrids. Ligation of the coding sequences to transcriptional regulatory elements or to other amino acid encoding sequences can be carried out using established methods. A large number of vectors, including bacterial, fungal, yeast, and mammalian vectors, have been described for replication and/or expression in various host cells or cell-free systems, and may be used with the secretion sequences described herein for simple cloning or protein expression.
Certain embodiments may employ fungal promoters or regulatory elements. For example, a promoter or regulatory element may comprise the CBH1 promoter from T. reesei and the trpC terminator from A. nidulans. The efficiency of expression may be enhanced by the inclusion of enhancers that are appropriate for the particular fungal cell system which is used, such as those described in the literature.
It will be appreciated by one skilled in the art that use of recombinant DNA technologies can improve control of expression of transformed nucleic acid molecules by manipulating, for example, the number of copies of the nucleic acid molecules within the host cell, the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications. Additionally, the promoter sequence might be genetically engineered to improve the level of expression as compared to the native promoter. Recombinant techniques useful for controlling the expression of nucleic acid molecules include, but are not limited to, integration of the nucleic acid molecules into one or more host cell chromosomes, addition of vector stability sequences to plasmids, substitutions or modifications of transcription control signals (e.g., promoters, operators, enhancers), substitutions or modifications of translational control signals (e.g., ribosome binding sites), modification of nucleic acid molecules to correspond to the codon usage of the host cell, and deletion of sequences that destabilize transcripts.
The nucleic acids, including parts or all of expression vectors, may be isolated directly from cells, or, alternatively, the polymerase chain reaction (PCR) method can be used to produce the nucleic acids. Primers used for PCR can be synthesized using the sequence information provided herein and can further be designed to introduce appropriate new restriction sites, if desirable, to facilitate incorporation into a given vector for recombinant expression. The nucleic acids can be produced in large quantities by replication in a suitable host cell (e.g., prokaryotic or eukaryotic cells such as bacteria, fungi, yeast, insect or mammalian cells). The production and purification of nucleic acids are described, for example, in Sambrook et al., 1989; F. M. Ausubel et al., 1992, Current Protocols in Molecular Biology, J. Wiley and Sons, New York, N.Y.
The nucleic acids described herein may be used in methods for production of chimeric Ce17A polypeptides through incorporation into cells, tissues, or organisms. In some embodiments, a nucleic acid may be incorporated into a vector for expression in suitable host cells. The vector may then be introduced into one or more host cells by any method known in the art. One method to produce an encoded protein includes transforming a host cell with one or more recombinant nucleic acids (such as expression vectors) to form a recombinant cell. The term “transformation” is generally used herein to refer to any method by which an exogenous nucleic acid molecule (i.e., a recombinant nucleic acid molecule) can be inserted into a cell, but can be used interchangeably with the term “transfection.”
In additional embodiments, the activity of a Ce17A polypeptide may be increased by expressing a nucleic acid encoding the Ce17A polypeptide in a heterologous host cell and isolating the Ce17A polypeptide from the cell. For example, the expression of wild-type P. funiculosum Ce17A in T. reesei may result in a Cella polypeptide with higher activity than wild-type P. funiculosum Ce17A expressed in or isolated from native wild-type P. funiculosum cells. Such increased activity can be seen in the experiments described in Example 7. Without wishing to be bound by any one theory, this observed activity increase may be due to differences in glycosylation patterns with glycans playing some role here in altering enzyme activity. Methods of making these improved Ce17A polypeptides and improved Ce17A polypeptides expressed in heterologous host cells are additional embodiments contemplated herein. In certain embodiments, the Ce17A polypeptide, such as P. funiculosum Ce17A, is expressed in T. reesei. 
Non-limiting examples of suitable host cells include cells from microorganisms such as bacteria, yeast, fungi, and filamentous fungi. Exemplary microorganisms include, but are not limited to, filamentous fungi from the genera Trichoderma (e.g., T. reesei, T. viride, T. koningii, or T. harzianum), Penicillium (e.g., P. funiculosum), Humicola (e.g., H. insolens), Chrysosporium (e.g., C. lucknowense), Gliocladium, Aspergillus (e.g., A. niger, A. nidulans, A. awamori, or A. aculeatus), Fusarium, Neurospora, Hypocrea (e.g., H. jecorina), and Emericella; yeasts from the genera Saccharomyces (e.g., S. cerevisiae), Pichia (e.g., P. pastoris), or Kluyveromyces (e.g., K. lactis). Cells from plants such as Arabidopsis, barley, citrus, cotton, maize, poplar, rice, soybean, sugarcane, wheat, switch grass, alfalfa, miscanthus, and trees such as hardwoods and softwoods are also contemplated herein as host cells.
Host cells can be transformed, transfected, or infected as appropriate by any suitable method including electroporation, calcium chloride-, lithium chloride-, lithium acetate/poly ene glycol-, calcium phosphate-, DEAE-dextran-, liposome-mediated DNA uptake, spheroplasting, injection, microinjection, microprojectile bombardment, phage infection, viral infection, or other established methods. Alternatively, vectors containing the nucleic acids of interest can be transcribed in vitro, and the resulting RNA introduced into the host cell by well-known methods, for example, by injection. Exemplary embodiments include a host cell or population of cells expressing one or more nucleic acid molecules or expression vectors described herein (for example, a genetically modified microorganism). The cells into which nucleic acids have been introduced as described above also include the progeny of such cells.
Vectors may be introduced into host cells such as those from filamentous fungi by direct transformation, in which DNA is mixed with the cells and taken up without any additional manipulation, by conjugation, electroporation, or other means known in the art. Expression vectors may be expressed by filamentous fungi or other host cells episomally or the gene of interest may be inserted into the chromosome of the host cell to produce cells that stably express the gene with or without the need for selective pressure. For example, expression cassettes may be targeted to neutral chromosomal sites by recombination.
Host cells carrying an expression vector (i.e., transformants or clones) may be selected using markers depending on the mode of the vector construction. The marker may be on the same or a different DNA molecule. In prokaryotic hosts, the transformant may be selected, for example, by resistance to ampicillin, tetracycline or other antibiotics. Production of a particular product based on temperature sensitivity may also serve as an appropriate marker.
Host cells may be cultured in an appropriate fermentation medium. An appropriate, or effective, fermentation medium refers to any medium in which a host cell, including a genetically modified microorganism, when cultured, is capable of growing or expressing the chimeric polypeptides described herein. Such a medium is typically an aqueous medium comprising assimilable carbon, nitrogen and phosphate sources, but can also include appropriate salts, minerals, metals and other nutrients. Microorganisms and other cells can be cultured in conventional fermentation bioreactors and by any fermentation process, including batch, fed-batch, cell recycle, and continuous fermentation. The pH of the fermentation medium is regulated to a pH suitable for growth of the particular organism. Culture media and conditions for various host cells are known in the art. A wide range of media for culturing filamentous fungi, for example, are available from ATCC. Exemplary culture/fermentation conditions and reagents are provided in the Examples that follow.
The nucleic acid molecules described herein encode chimeric Ce17A polypeptides with amino acid sequences such as those represented by SEQ ID NO:6, 8, 10, 12, 14 and 16. As used herein, the terms “protein” and “polypeptide” are synonymous. “Peptides” are defined as fragments or portions of polypeptides, preferably fragments or portions having at least one functional activity as the complete polypeptide sequence. “Isolated” proteins or polypeptides are proteins or polypeptides purified to a state beyond that in which they exist in cells. In certain embodiments, they may be at least 10% pure; in others, they may be substantially purified to 80% or 90% purity or greater. Isolated proteins or polypeptides include essentially pure proteins or polypeptides, proteins or polypeptides produced by chemical synthesis or by combinations of biological and chemical methods, and recombinant proteins or polypeptides that are isolated. Proteins or polypeptides referred to herein as “recombinant” are proteins or polypeptides produced by the expression of recombinant nucleic acids.
Proteins or polypeptides encoded by nucleic acids as well as functional portions or variants thereof are also described herein. Polypeptide sequences may be identical to the amino acid sequence of SEQ ID NO:6, 8, 10, 12, 14 or 16, or may include up to a certain integer number of amino acid alterations. Such protein or polypeptide variants retain functionality as cellulases, and include mutants differing by the addition, deletion or substitution of one or more amino acid residues, or modified polypeptides and mutants comprising one or more modified residues. The variant may have one or more conservative changes, wherein a substituted amino acid has similar structural or chemical properties (e.g., replacement of leucine with isoleucine). Alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the reference sequence or in one or more contiguous groups within the reference sequence.
In certain embodiments, the polypeptides may be at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO:6, 8, 10, 12, 14 or 16 and possess cellulase function. Percent sequence identity can be calculated using computer programs (such as the BLASTP and TBLASTN programs publicly available from NCBI and other sources) or direct sequence comparison. Polypeptide variants can be produced using techniques known in the art including direct modifications to isolated polypeptides, direct synthesis, or modifications to the nucleic acid sequence encoding the polypeptide using, for example, recombinant DNA techniques.
Modified polypeptides, including those with post-translational modifications, are also contemplated herein. Isolated polypeptides may be modified by, for example, phosphorylation, methylation, farnesylation, carboxymethylation, geranyl geranylation, glycosylation, acetylation, myristoylation, prenylation, palmitation, amidation, sulfation, acylation, or other protein modifications. They may also be modified with a label capable of providing a detectable signal, either directly or indirectly, including, but not limited to, radioisotopes and fluorescent compounds. The polypeptides may be useful as antigens for preparing antibodies by standard methods. Monoclonal and polyclonal antibodies that specifically recognize the polypeptides disclosed herein are contemplated.
Chimeric polypeptides such as those represented by SEQ ID NO:6, 8, 10, 12, 14 or 16 may be expressed, isolated and used as stand-alone polypeptides. They may also be fused to one or more additional polypeptides (using, for example, recombinant technology) to create a fusion protein with an additional complete polypeptide or a functional domain of a polypeptide. Suitable fusion segments include segments that can enhance a protein's stability, provide other desirable biological activity, or assist with the purification of the protein (e.g., by affinity chromatography). A suitable fusion segment can be a domain of any size that has the desired function (e.g., imparts increased stability, solubility, action or biological activity; or simplifies purification of a protein).
Chimeric polypeptides may be detected by any assay known in the art to detect a protein of interest. Examples include enzymatic activity assays, detection with specific antibodies (immunoblotting, ELISA, etc.), and other suitable detection techniques.
Chimeric polypeptides may also be isolated or recovered from the media used in host cell cultures or cell-free expression systems. The phrase “recovering the protein” refers to collecting the whole culture medium containing the protein and need not imply additional steps of separation or purification. Proteins can be purified using a variety of standard protein purification techniques, such as affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing, differential solubilization, preparative disc-gel electrophoresis, isoelectric focusing, HPLC, reversed-phase HPLC, or countercurrent distribution. The polypeptide may contain an additional protein or epitope tag that facilitates detection or purification, such as c-myc, haemagglutinin (HA), polyhistidine, GLU-GLU, FLAG-tag, glutathione-S-transferase (GST), green fluorescent protein (GFP), or maltose binding protein (MBP). Such tags may be removed following the recovery of the polypeptide.
Polypeptides may be retrieved, obtained, or used in “substantially pure” form, a purity that allows for the effective use of the protein in any method described herein or known in the art. For a protein to be most useful in any of the methods described herein or in any method utilizing enzymes of the types described herein, it is most often substantially free of contaminants, other proteins and/or chemicals that might interfere or that would interfere with its use in the method (e.g., that might interfere with enzyme activity), or that at least would be undesirable for inclusion with a protein.
Methods for degrading cellulose and materials containing cellulose using the chimeric Ce17A polypeptides are also provided herein. For example, the chimeric Ce17A polypeptides may be used in compositions to help degrade (e.g., by liquefaction) a variety of cellulose products (e.g., paper, cotton, etc.) in landfills. The chimeric Ce17A polypeptides may also be used to enhance the cleaning ability of detergents, function as a softening agent or improve the feel of cotton fabrics (e.g., stone washing or biopolishing) or in feed compositions.
Cellulose containing materials may also be degraded to sugars using the chimeric Ce17A polypeptides. Ethanol may be subsequently produced from the fermentation of sugars derived from the cellulosic materials. Exemplary cellulose-containing materials include bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, wood and forestry waste. Examples of biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, corn fiber, grasses, wheat, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood (e.g., poplar) chips, sawdust, shrubs and bushes, vegetables, fruits, flowers and animal manure.
Biofuels such as ethanol may be produced by saccharification and fermentation of lignocellulosic biomass such as trees, herbaceous plants, municipal solid waste and agricultural and forestry residues. Typically, saccharification is carried out by contacting the lignocellulosic biomass with an enzyme cocktail that includes one or more Family 7 cellulases such as the chimeric Ce17A polypeptides described herein. Such enzyme cocktails may also contain one or more endoglucanases (such as the Family 5 endoglucanase E1 from Acidothermus cellulolyticus) or one or more β-glucosidases (e.g., a β-glucosidase from A. niger) to optimize hydrolysis of the lignocelluloses. Additional suitable endoglucanases include EGI, EGII, EGIII, EGIV, EGV or Ce17B (e.g., Ce17B from T. reesei). Enzyme cocktails may also include accessory enzymes such as hemicellulases, pectinases, oxidative enzymes, and the like.
Enzymes with the ability to degrade carbohydrate-containing materials, such as cellulases with endoglucanase activity, exoglucanase activity, or β-glucosidase activity, or hemicellulases with endoxylanase activity, exoxylanase activity, or β-xylosidase activity may be included in enzyme cocktails. Examples include enzymes that possess cellobiohydrolase, α-glucosidase, xylanase, β-xylosidase, α-galactosidase, β-galactosidase, α-amylase, glucoamylases, arabinofuranosidase, mannanase, β-mannosidase, pectinase, acetyl xylan esterase, acetyl mannan esterase, ferulic acid esterase, coumaric acid esterase, pectin methyl esterase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-β-D-glucosaminidase, cellobiose dehydrogenase, ligninase, amylase, glucuronidase, ferulic acid esterase, pectin methyl esterase, arabinase, lipase, glucosidase or glucomannanase activities.
A lignocellulosic biomass or other cellulosic feedstock may be subjected to pretreatment at an elevated temperature in the presence of a dilute acid, concentrated acid or dilute alkali solution for a time sufficient to at least partially hydrolyze the hemicellulose components before adding the enzyme cocktail. Additional suitable pretreatment regimens include ammonia fiber expansion (AFEX), treatment with hot water or steam, or lime pretreatment.
Separate saccharification and fermentation is a process whereby cellulose present in biomass is converted to glucose that is subsequently converted to ethanol by yeast strains. Simultaneous saccharification and fermentation is a process whereby cellulose present in biomass is converted to glucose and, at the same time and in the same reactor, converted into ethanol by yeast strains. Enzyme cocktails may be added to the biomass prior to or at the same time as the addition of a fermentative organism.
The resulting products after cellulase degradation may also be converted to products other than ethanol. Examples include conversion to higher alcohols, hydrocarbons, or other advanced fuels via biological or chemical pathways, or combination thereof.
EXAMPLES
Example 1
Construction of Expression Vectors
An expression vector was designed, designated pTREXP002, which contains the expression cassette for the A. nidulans AMDS gene allowing for growth on acetamide as the sole nitrogen source. DNA encoding the chimeric Ce17A proteins were synthesized and subcloned in this plasmid between the CBH1 promoter from T. reesei and the trpC terminator from A. nidulans. The insertion of target genes in the correct orientation was confirmed by PCR and digestion with restriction enzymes. Plasmid DNAs prepared from E. coli were used for transformation of T. reesei. 
The expression vector pTr50 was developed for expression of chimeric genes in the cbh1Δ T. reesei strain AST1116. This vector uses hpt gene from E. coli as the selection marker and the expression of desired genes is driven by the T. reesei cbh1 promoter. A diagram of this vector is presented in FIG. 10.
All restriction enzymes, T4 DNA ligase, Taq DNA polymerase and related buffers and chemicals were obtained from New England Biolabs (Beverly, Mass., USA). Plasmid constructions, E. coli transformations, DNA isolation and other DNA manipulation techniques were used as described in standard protocols. The oligonucleotide primers used in this study are listed below in Table 2.










TABLE 2








SEQ 


Name
Sequence
Description
ID NO:







AS096
TGCTCTTTTGAGCT
5′primer external
17



ACAAGAACCTGTGG
to cbh1 deletion





cassette for Rut C-30



 


AS097
GAACAAGCTTTTTGG
3′primer external
18



CATCGTGGATCCATT
to cbh1 deletion





cassette for Rut C-30



 


AS104
ACTTACTAGTATGCCTCA
5′primer to clone 
19



ATCCTGGGAAGAACTGG
Aspergillus





nidulans amdS gene



 


AS105
ATTGACTAGTCTATGGA
3′primer to clone 
20



GTCACCACATTTCCCAG
Aspergillus





nidulans amdS gene



 


AS113
CTGGAAAGTGACG
3′primer in cbh1 
21



CCATTCTGGACAT
CDS



 


AS117
ATGAAGAAGCCGG
5′primer inside 
22



AGTTGACTGCAAC
cbh1 CDS



 


AS120
CTCCCAGCTGA
5′primer inside 
23



CTGGCCAATTC
cbh1



 


AS123
CGGCTTCTTCATAC
3′primer spanning 
24



TAGTGGCAGGAAAT
PGK1 promoter and





E. coli hph CDS





in deletion cassette



 


AS133
AGCACTCTCTCG
5′primer external 
25



CCCAATGATGTC
to cbh1 deletion





cassette for QM6a



 


AS134
TCCGACTCTTTTAA
3′primer in PGK1p 
26



TCATCGCGTATATCC
in deletion





cassette for QM6a



 


AS135
AAGAGTATGATCC
5′primer in amdS 
27



GGAGGCGTACCA
CDS in deletion 





cassette for QM6a



 


AS136
CCAATAATACATTAAC
3′primer external 
28



AACACAGTTTCAGCCC
to cbh1 deletion





cassette for QM6a









Example 2
Transformation of T. reesei 
Potato dextrose (PD), obtained from Sigma, and Complete Medium with lactose (CML) were used as the routine culture media. PDA (PD with agar) was used for sporulation of various Trichoderma strains. The CML medium contained, per liter: yeast extract (5 g) tryptone (5 g), lactose (10 g) and Clutterbuck's salts. The pH of this medium was adjusted to 7.5 with KOH. The minimal medium (MMA) for growth on acetamide for nitrogen source contained, per liter: glucose (20 g), KH2PO4 (15 g), MgSO4 (0.6 g), CaCl2 (0.6 g), sorbitol (182.2 g), acetamide (0.59 g), CsCl (2.10 g), Agar (20 g), FeSO4.7H2O (0.005 g), MnSO4.H2O (0.0016 g), ZnSO4.7H2O (0.0014 g) and CoCl2 (0.002 g). For solidification, all media contained 2% agar. For spheroplast transformation, CML, PDA and MMA contained 1 M sorbitol. All cultures of T. reesei were grown at 30° C. The liquid cultures were grown in shake flasks with shaking at 225 rpm.
T. reesei spheroplasts were prepared and transformed with slight modifications of published methods (See Penttila et al. (Gene 61:155 (1991)). Spheroplasts were generated from 30-48 hour cultures in PD or CML started with spore stocks. Mycelia were collected by filtration through Mira cloth, washed with water and incubated in 0.6M KCl containing 3 mg/ml Glucanex (Sigma) and 2 mg per ml lysozyme (Sigma) for 3-4 hours at 30° C. with gentle shaking (90 rpm). After 7 hours of recovery period of transformed spheroplasts in rich medium, PD or CML, the hygromycin-B-resistant transformants were selected by mixing the transformed spheroplasts with 10 ml of PD or CML agar media containing 1.0M sorbitol and 100 mg/L hygromycin B and pouring over Petri dishes containing the same medium. The spheroplasts transformed for ability to utilize acetamide as sole nitrogen source were selected on the MMA media containing acetamide as the sole nitrogen following the protocol described by Penttila et al. Transformants were purified by two rounds of sporulation and testing of single spores for resistance to hygromycin B or ability to use acetamide as the sole nitrogen source.
Example 3
Strains and Cultivation for Expression of Proteins
The Trichoderma reesei strains, QM6a and Rut C-30, obtained from the American Type Culture Collection, were used as the base strains from which the expression strains were constructed. The cbh1 CDS and cbh1 promoter were deleted in QM6a to create the cbh1Δ strain, AST1116.
T. reesei Rut C-30 was used both in wild type form as well as genetically altered form for cellulase production. Seed cultures were prepared in triplicate by soaking the spores for 48 hours in tissue culture tubes at 30° C. at 150 rpm in 5 mL containing Vogel minimal media with a 2.5% w/v glucose solution. Subsequently, the seed cultures were used to inoculate 500 mL of Vogel's minimal media with a 2.5% w/v glucose solution for an additional 72 hours. Vogel's 50× salts were used, which consisted of 150 g Na3 citrate.2H2O, 250 g of KH2PO4, 100 g of NH4NO3, 10 g of MgSO4, 5 g of CaCl2, 5 ml of trace element solution and 2.5 mL of a 1% w/v Botin solution dissolved into 750 mL of distilled water. The trace elements consisted of 5 g of citric acid.1H2O, 5 g ZnSO4.7H2O, 1 g of Fe(NH4)2(SO4)2.6H2O, 0.25 g of CuSO4.5H2O, 0.05 g of MnSO4.1H2O, 0.05 g of anhydrous H3BO3, and 0.05 g of Na2MoO4.2H2O dissolved into 95 mL of distilled water. These seed cultures were transferred to a 1 L shake flask (500 mL actual volume) and incubated at 30° C. at 150 rpm. After 72 hours of growth in the shake flasks, the fungal broths were screened for any potential contamination and one of the 1 L shakes flasks was used to inoculate the fermentor. The other shake flasks received 60 mL of 20% w/v lactose resulting in a final lactose concentration of approximately 2% w/v. These shake flasks were then incubated for an additional 96 hours at 30° C. at 150 rpm.
Example 4
Fermentations for Expression of Proteins
The fermentations were performed in both 5 and 3 L New Brunswick scientific Bioflow 3000 fermentors with an operating volume of 4 and 2 L, respectively. Vogel's minimal media was chosen to use in the fermentors due to the low foaming associated with this media. The fermentation temperature was maintained at 30° C. and the pH was maintained between 5.0 and 5.6 depending on the initial pH of the fermentor after inoculation. The pH was maintained using 1 M KOH and 1 M HCl via a computer controlled feedback system. During the initial phase of the fermentation, the acid feedback control was turned off, and turned on again when the system began to run low on nutrients. The amount of foam was controlled with the use of Sigma Aldrich Antifoam 204 and the dissolved oxygen was controlled via a feedback system with the setting of 30% dissolved oxygen relative to air.
The glucose concentration was monitored by taking time points throughout the fermentation and then measuring the glucose concentration via Megazyme GOPOD. The main goal with these fermentations was to obtain a large amount of fungal mass with glucose and as the glucose concentration dwindled, we began feeding lactose to the system to produce a lactose limited batch of proteins. The dissolved oxygen probes were not reliable enough to control the feeding of a 5% w/v lactose solution. Therefore the lactose solution was fed at a constant rate of 1 mL/min once the glucose concentration reached approximately 0.7%. After this, the lactose concentration was monitored using Megazyme Lactose and D-Galactose assay. The goal was to keep the lactose at a concentration between 0.5% and 1% w/v during the rest of the fermentation. During this phase, we monitored the production of the chimeras via measuring the activity on PnPl. Once the activity on PnPl leveled off, the fermentations were stopped, and the fungal broths were filtered and concentrated. The remaining shake flasks were harvested to verify protein production within the chimera in the event the fermentation failed signaling that the lack of protein expression was due to a bad fermentation run and not because the chimera strain failed to express.
For additional fermentations, the transformed cell culture was streaked on a Potato Dextrose Agar plate and allowed to grow 2-3 days until a well lawn plate of spores was achieved. An approximately 0.5 cm plug was extracted from the plate and deposited into 50 ml of liquid growth media in a 250 mL shake flask. The growth media consisted of Mandel's Growth Media with 5% lactose as the carbon source in lieu of glucose, and 0.5% tryptone added. The culture was grown at 28° C. with agitation for 48 hours, whereupon the entire 50 mL was transferred to 1 L of the same media, in a 2.8 L shake flask. The culture was again grown at 28° C. with agitation for 3 days, after which the entire 1 L was transferred to 7 L of the same media, in a bioreactor. The bioreactors were 15 L working volume vessels manufactured by New Brunswick and controlled via New Brunswick's BioFlo3000 system. The total of 8 L was grown with mixing at 200 rpm via rushton style impellers, purged with 1.0 L/min of filtered air, kept at a strict 28° C., and pH controlled at 4.8. The acid and base used for pH control was HCl and KOH, respectively. The cell culture was grown for 4 days, after which the entire culture broth was drained, filtered through nylon to remove all cell mass, and concentrated via tangential flow filtration. The concentrated broth was buffer exchanged into 20 mM Bis-Tris pH 6.5, and brought up to about 200 mL, where it was then subjected to purification.
Example 5
Purification of Proteins
Culture supernatants were collected as follows. Mycelial mass was removed by gravity filtration using Miracloth (EMD Biosciences, Gibbstown, N.J.). The supernatant obtained was passed, under vacuum, through a series of glass fiber filters with descending pore sizes ranging from 2.7 μm to 0.7 μm (Millipore, Billerica, Mass.). This was followed by vacuum filtration through 0.45 μm and 0.2 μm bottle-top filtration devices (Nalgene, Rochester, N.Y.). After filtration, supernatants were concentrated to about 1/50th original volume and exchanged into 20 mM Bis-Tris, pH 6.5.
The concentrated supernatants were amended to 2 M NH4SO4 by addition of an equal volume of 30 mM Bis-Tris pH 5.8, 4 M NH4SO4, loaded onto a Tricorn 10/100 column (GE Healthcare, Piscataway, N.J.) packed with Source 15Phe Hydrophobic Interaction Chromatography medium (GE Healthcare), and eluted using a 25 column volume linear gradient of 20 mM Bis-Tris, pH 5.8, 2M NH4SO4. Fractions were assayed for Ce17A activity by adding 25 μL of each fraction to 150 μL of a solution of 2 mM p-nitrophenol-β-lactopyranoside (pNPL; Sigma-Aldrich, St. Louis, Mo.) in 50 mM Sodium Acetate, pH 5.0 in a microtiter plate. Reactions were incubated 30 min at 45° C. and quenched by addition of 25 μL 1 M sodium carbonate. Absorbance was read at 405 nm with absorbances compared to a standard curve of p-nitrophenol in 50 mM sodium acetate pH 5.0. Fractions with significant pNPL activity were pooled and examined by SDS-PAGE and western blotting using polyclonal antibodies raised against the catalytic domain of T. reesei or P. funiculosum Ce17A, as required. Pooled peaks containing rCe17A were desalted into 20 mM Bis-Tris, pH 6.5 using two Hi Prep 26/10 desalting columns in series. The resultant protein solution was loaded onto a Tricorn 10/100 column packed with Source 15Q anion-exchange medium (GE Healthcare) and eluted with a 20 column volume linear gradient of 20 mM Bis-Tris pH 6.5, 1M NaCl. Fractions were assayed and visualized as above, concentrated to a volume less than 13 mL in 10 kDa MWCO Amicon Centricon Plus-20 centrifugal concentration devices and loaded onto a HiLoad Superdex75 26/60 size exclusion column and eluted at 1 mL/min in 20 mM Sodium Acetate, pH 5.0, 100 mM NaCl. Fractions were assayed and visualized as above, pooling fraction containing a single, western blot positive band. The purified rCe17A solution obtained was quantified using the bicinchoninic acid protein assay (Pierce, Rockford, Ill.).
Example 6
Activity Assays
Cellobiohydrolase activity was measured as the saccharification of the cellulose fraction of a sample of a standard dilute-acid-pretreated corn stover by the cellobiohydrolase when used in conjunction with two other enzymes at standard loadings (1) the endoglucanase Acidothermus cellulolyticus E1 (Ce15A, catalytic domain) loaded at 1.894 mg/g of biomass cellulose and (2) the chromatographically-purified beta-glucosidase from Aspergillus niger, loaded at 2.0 mg/g biomass cellulose.
The standard biomass substrate used in the activity assays is NREL dilute-acid-pretreated corn-stover P050921, washed first with water and then with 20 mM acetic acid/sodium acetate buffer, pH 5.0, until the pH of the (buffer) decantate is within 0.03 units of 5.00. From a slurry of this washed biomass material (approximately 9 mg biomass per mL of pH 5.0, 20 mM acetate buffer containing 0.02% sodium azide to retard microbial growth), a series of biomass substrate aliquots were prepared in 2.0-mL HPLC vials, in such a way that each vial contains 8.5 mg biomass cellulose (which, given that the “glucan” content of this batch of pretreated stover is 59.1%, requires 14.38 mg of biomass per digestion vial). Biomass dry weights for each batch of assay vials were verified by dry-weight determinations on a group of five samples co-pipetted into pre-tared vials. The acceptable relative standard deviation for a batch of biomass assay aliquots is 1% or less, with a preferred value of 0.8% or less. Adjustment of these biomass assay aliquots to a 1.7-mL final volume results in a cellulose concentration of 5 mg/mL.
Cellobiohydrolase assays were conducted in triplicate vials at 40° C., pH 5.0 in 20 mM azide-containing acetate buffer, with continuous mixing by inversion at 10 rpm while immersed in a water bath. At various times during the digestion, the vials were removed from the rotator, representative 100-μL samples containing both solids and liquid were removed from the well-stirred contents and diluted 18-fold into glass HPLC vials. The primary digestion vials were immediately resealed and returned to the rotator in the assay 40° C. water bath so that the assay digestions may continue. The vials containing the withdrawn and diluted samples of digestion mixture were then crimp-sealed and immersed in a boiling-water bath for 10 minutes to denature the enzymes and terminate the reaction. The contents of the boiled time-sample vials were then syringe-filtered (0.2-micron Acrodisc) into a third set of vials for sugar analysis by HPLC on a BioRad HPX-87H column operated at 65° C. with 0.01 N H2SO4 as the eluent at 0.6 mL/min and refractive-index detection. Values for individual sugar concentrations in the digestion vials were back-calculated from the values measured by HPLC, and then used to construct saccharification progress-curves in terms of percent of conversion of biomass cellulose.
The “standard performance” against which cellobiohydrolase performances are measured is that of T. reesei Ce17A when loaded at 46.68 mg per g cellulose, along with the two standard adjuvant enzymes described above, acting against the substrate aliquots described above. At this loading, and under these conditions, the T. reesei enzyme will catalyze conversion of 80% and 90% of the biomass cellulose in the process-relevant digestion times of slightly over one day and approximately 2.5 days, respectively. Activity comparisons of engineered cellobiohydrolases with that of the standard T. reesei Ce17A are conducted in two stages. First, the mutant cellobiohydrolases assayed at the same loading (46.68 mg/g cellulose) as that used to measure the activity of the standard T. reesei Ce17A with assays continued until all enzymes have achieved 80% or more saccharification of the biomass cellulose.
From the interpolated times of intersection of the respective progress curves with the “80%-conversion” line, a preliminary estimate was made of the loading of the cellobiohydrolase mutant required to reach 80% conversion in the same digestion time that the standard T. reesei enzyme, at its standard loading, requires to reach this extent of conversion. This first estimate was based on the assumption, which is mathematically demonstrated for simple systems involving single enzymes and uniformly available soluble substrates, and which been rather well supported by experiments involving more complicated systems, that the reaction time required for a given enzyme to convert a certain proportion of a given initial quantity of substrate is inversely proportional to the enzyme loading.
On the basis of the first estimate of Ce17A-equivalence, an additional experimental series was designed to yield a more precise estimate (one not involving the extrapolations involved in the first estimate). A series of loadings (typically four or five) of the cellobiohydrolase mutant was setup to bracket closely the “T. reesei-Ce17A-equivalent” loading estimated by the first experimental series, with conversion data being collected for the mutant enzyme and for a standard T. reesei control in the time-frame in which the T. reesei control would be expected to achieve conversion near 80%. Interpolation in a plot of actual conversion by the mutant enzyme as a function of enzyme loading (FIG. 11), for a given digestion time, was then used to yield a more precise estimate of the loading of the “new” enzyme that would be required to give the same conversion as that delivered by the standard loading of T. reesei CBHI. As shown in FIG. 11, approximately 15 mg of the T-T-P chimera per g of cellulose achieved 80% conversion at 27 hours, as compared to 46.68 mg of the wild-type T. reesei control per g of cellulose (horizontal line).
Example 7
Activity of Chimeric Enzymes
To engineer enhanced cellobiohydrolases, and to understand the role of the individual sub-domains in processive hydrolysis, the domains of the T. reesei Ce17A enzyme were swapped with those from the P. funiculosum Ce17A. The P. funiculosum enzyme exhibits somewhat higher activity than the T. reesei Ce17A enzyme, but the mechanistic basis for the activity differences remains unknown. Table 3 shows the chimeric enzymes screened for activity in this study. These enzymes were expressed in a strain of T. reesei lacking the native Ce17A gene, as described above. T=T. reesei and P=P. funiculosum.









TABLE 3







Catalytic


CBM
Linker
Domain







T
T
T


P
P
P


T
T
P


P
P
T


P
T
P









Several of the Family 7 cellulases listed in Table 3 were screened on dilute acid pretreated corn stover at a loading of 46 mg of total enzyme per gram of cellulose. For synergy purposes, we added a Family 5 endoglucanase, E1 from Acidothermus cellulolyticus and a β-glucosidase from Aspergillus niger. The results from the screening are shown in FIG. 12. Cellulase activity is compared as the time to reach 80% conversion, which is the target conversion for industrial-scale biochemical conversion processes. FIG. 12 shows that the T-T-P Ce17A chimera has a substantially higher activity than either the T. reesei Ce17A or P. funiculosum Ce17A controls. Based on the time to reach 80% conversion, the T-T-P chimera exhibits a 3.1-fold improvement in activity at the same loading over the wild-type T. reesei Ce17A. Moreover, domain-swapping of these enzymes produced an enzyme with higher activity than the parent enzymes. This result shows, for the first time, that significant activity improvements can be made to Family 7 cellulases, which are the cornerstone of modern enzyme cocktails for production of sugars from lignocellulosic biomass. Additional chimera activity data are presented in FIGS. 13, 14 and 15.
FIG. 14 illustrates a comparison of the time required for the T-T-P chimera and wild-type T. reesei Ce17A to reach 80% conversion of pretreated corn stover cellulose. Both enzymes were loaded at 8.94 mols/g cellulose (corresponds to 46.7 mg/g cellulose for wild-type T. reesei Ce17A) in combination with 1.894 mg A. cellulolyticus E1 (CD domain) and 2.0 mg A. niger β-glucosidase per g cellulose. The substrate was 5.03 mg/mL cellulose (dilute-acid-pretreated corn stover—59.07% cellulose), pH 5.0 in 20-mM acetate. Assays were carried out at 40° C. with constant mixing by inversion 10 min−1 and conversion was monitored by HPLC analysis of released sugars. As depicted in FIG. 14, the T-T-P chimera reaches 80% conversion almost three times faster than the wild-type T. reesei Ce17A.
FIG. 15 compares the amount of time to reach 80% conversion of pretreated corn stover cellulose for wild-type T. reesei Ce17A (46 mg/g cellulose) and the T-T-P chimera at various enzyme loadings (24, 18, 12, 9 and 6 mg/g cellulose). The data show that significantly less T-T-P chimera enzyme is needed to reach 80% conversion within the same amount of time.
As shown in FIG. 16, four enzymes were assayed at a molar loading of 0.45 μmol enzyme per gram of pretreated corn stover cellulose. This corresponds to approximately 23-24 mg of enzyme per gram of cellulose for each assay. In addition to the natively expressed P. funiculosum wild type Ce17A enzyme (Pfun WT), the T-T-P chimera, the P-T-P chimera and P-P-P enzyme (P. funiculosum wild type Ce17A expressed in T. reesei) were tested. As with the above chimeras, each of the two chimeric enzymes in this assay was expressed in T. reesei. 
The results shown in FIG. 16 demonstrate that T-T-P chimera (about 19 hours) and the P-T-P chimera (about 16.5 hours) require much less time to reach 80% conversion of cellulose than the natively expressed P. funiculosum wild type Ce17A enzyme (about 65 hours) or the P. funiculosum wild type Ce17A expressed in T. reesei (about 31.7 hours) at an equivalent enzyme loading. Further, the P. funiculosum wild type Ce17A expressed in T. reesei requires less time to reach 80% conversion of cellulose than the natively expressed P. funiculosum wild type Ce17A enzyme.
The Examples discussed above are provided for purposes of illustration and are not intended to be limiting. Still other embodiments and modifications are also contemplated.
While a number of exemplary aspects and embodiments have been discussed above, those of skill in the art will recognize certain modifications, permutations, additions and sub combinations thereof. It is therefore intended that the following appended claims and claims hereafter introduced are interpreted to include all such modifications, permutations, additions and sub-combinations as are within their true spirit and scope.

## Claims

1. An isolated nucleic acid molecule encoding a chimeric fungal CeI7A polypeptide that has a cellulase activity at least 1.5-fold greater than the wild-type CeI7A polypeptide, wherein the chimeric CeI7A polypeptide comprises the following domains: a catalytic domain (CD), a carbohydrate-binding module (CBM) and a linker domain, and wherein at least one of the domains is from a Penicillium funiculosum CeI7A polypeptide and at least one of the domains is from a Trichoderma reesei CeI7A polypeptide; and wherein each domain is from the Penicillium funiculosum or Trichoderma reesei CeI7A polypeptides.

2. The isolated nucleic acid molecule of claim 1, wherein the chimeric CeI7A polypeptide comprises the catalytic domain (CD) from the Penicillium funiculosum CeI7A polypeptide.

3. The isolated nucleic acid molecule of claim 2, wherein the chimeric CeI7A polypeptide further comprises the carbohydrate-binding module (CBM) from the Trichoderma reesei CeI7A polypeptide.

4. The isolated nucleic acid molecule of claim 3, wherein the chimeric CeI7A polypeptide further comprises the linker domain from the Penicillium funiculosum CeI7A polypeptide.

5. The isolated nucleic acid molecule of claim 1, wherein the chimeric CeI7A polypeptide comprises the carbohydrate-binding module (CBM) from the Trichoderma reesei CeI7A polypeptide.

6. The isolated nucleic acid molecule of claim 1, wherein the chimeric CeI7A polypeptide has the amino acid sequence of SEQ ID NOS:6, 8, 10, 12, 14 or 16.

7. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid molecule has the sequence of SEQ ID NOS:5, 7, 9, 11, 13 or 15.

8. The isolated nucleic acid molecule of claim 1, further comprising a promoter operably linked to the nucleic acid molecule.

9. The isolated nucleic acid molecule of claim 8, wherein the promoter allows expression of the nucleic acid in a filamentous fungal host cell.

10. An expression vector comprising the nucleic acid molecule of claim 1.

11. A host cell comprising the expression vector of claim 10 or expressing a recombinant polypeptide encoded by the nucleic acid molecule of claim 1.

12. The host cell of claim 11, wherein the cell is a fungal cell.

13. The host cell of claim 12, wherein the cell is from a strain of Trichoderma reesei.

14. The isolated nucleic acid molecule of claim 2, wherein the chimeric CeI7A polypeptide further comprises the linker domain from the Trichoderma reesei CeI7A polypeptide.

15. The isolated nucleic acid molecule of claim 14, wherein the chimeric CeI7A polypeptide further comprises the carbohydrate-binding module (CBM) from the Penicillium funiculosum CeI7A polypeptide.

16. The isolated nucleic acid molecule of claim 1, wherein the chimeric CeI7A polypeptide comprises the catalytic domain (CD) from the Trichoderma reesei CeI7A polypeptide.

17. The isolated nucleic acid molecule of claim 16, wherein the chimeric CeI7A polypeptide further comprises the linker domain from the Penicillium funiculosum CeI7A polypeptide.

18. The isolated nucleic acid molecule of claim 17, wherein the chimeric CeI7A polypeptide further comprises the carbohydrate-binding module (CBM) from the Penicillium funiculosum CeI7A polypeptide.

19. The isolated nucleic acid molecule of claim 1, wherein the chimeric fungal CeI7A polypeptide has a cellulase activity at least 2-fold greater than the wild-type CeI7A polypeptide.