title: Repair eXtreme - DNA repair proteins from Antarctic extremophiles

authors: Rzoska-Smith, Elizabeth

abstract: The McMurdo Dry valleys (DV) in Antarctica are one of the harshest environments on Earth, with high levels of UV radiation, freeze-thaw cycles, low moisture, and nutrient content. Bacteria in this extreme environment have adapted to slow growth and low-nutrient conditions. It is proposed that bacteria from Antarctic DV systems may possess unique DNA repair enzymes and pathways that enable their survival in such extreme conditions. Exploring these DNA repair systems may offer valuable insights into microbial survival in extreme environments or even extra-terrestrial settings. To investigate this, DNA repair enzymes were identified from Antarctic DV microbial metagenomes using in silico analysis and in vivo characterisation of recombinantly produced proteins.

Four candidate enzymes were chosen for structural and biological characterisation. Three of these enzymes are characterised as LigB type ATP-dependent DNA ligases, with the typical arrangement of a DNA binding domain, adenylation domain and an OB-fold domain. These ligases can utilise both ATP and ADP nucleotide cofactors for the ligation of nick and mismatch DNA substrates, requiring the addition of magnesium or manganese metal ions. One LigB ligase stands out due to its interesting fusion with an N-terminally located nuclease domain, which resembles an extensively studied MBL-β-CASP domain found in all domains of life. The recombinantly expressed nuclease domain can coordinate several types of metal ions and shows nuclease activity against a diverse range of DNA substrates. Nuclease activity favoured single-stranded DNA substrates, in a 5’ to 3’ direction, and was particularly active on substrates with abasic sites or 5’ flaps. The fourth protein was initially annotated as a hypothetical protein, however in silico analysis revealed that it exhibited homology to NucS nucleases identified in archaea and bacteria. This NucS homolog is a monomeric enzyme, made up of four domains, which is different from other proteins in this family. This enzyme shows a preference for single-stranded DNA and has a broad range of nuclease activity on damaged and mismatched DNA substrates. It can utilise both magnesium and manganese metal ions for activity on DNA substrates. Overall, these findings suggest that the described enzymes will play a role in DNA repair pathways, potentially in high-damage environments like the DVs of Antarctica.

text: Repair eXtreme - DNA repair proteins from Antarctic extremophiles The McMurdo Dry valleys (DV) in Antarctica are one of the harshest environments on Earth, with high levels of UV radiation, freeze-thaw cycles, low moisture, and nutrient content. Bacteria in this extreme environment have adapted to slow growth and low-nutrient conditions. It is proposed that bacteria from Antarctic DV systems may possess unique DNA repair enzymes and pathways that enable their survival in such extreme conditions. Exploring these DNA repair systems may offer valuable insights into microbial survival in extreme environments or even extra-terrestrial settings. To investigate this, DNA repair enzymes were identified from Antarctic DV microbial metagenomes using in silico analysis and in vivo characterisation of recombinantly produced proteins.

Four candidate enzymes were chosen for structural and biological characterisation. Three of these enzymes are characterised as LigB type ATP-dependent DNA ligases, with the typical arrangement of a DNA binding domain, adenylation domain and an OB-fold domain. These ligases can utilise both ATP and ADP nucleotide cofactors for the ligation of nick and mismatch DNA substrates, requiring the addition of magnesium or manganese metal ions. One LigB ligase stands out due to its interesting fusion with an N-terminally located nuclease domain, which resembles an extensively studied MBL-β-CASP domain found in all domains of life. The recombinantly expressed nuclease domain can coordinate several types of metal ions and shows nuclease activity against a diverse range of DNA substrates. Nuclease activity favoured single-stranded DNA substrates, in a 5’ to 3’ direction, and was particularly active on substrates with abasic sites or 5’ flaps. The fourth protein was initially annotated as a hypothetical protein, however in silico analysis revealed that it exhibited homology to NucS nucleases identified in archaea and bacteria. This NucS homolog is a monomeric enzyme, made up of four domains, which is different from other proteins in this family. This enzyme shows a preference for single-stranded DNA and has a broad range of nuclease activity on damaged and mismatched DNA substrates. It can utilise both magnesium and manganese metal ions for activity on DNA substrates. Overall, these findings suggest that the described enzymes will play a role in DNA repair pathways, potentially in high-damage environments like the DVs of Antarctica.

year: 2023

title: Soil and permafrost in the Ross Sea Region of Antarctica: Stable or dynamic?

authors: Balks, Megan R.

subjects: cryosol

abstract: Soils in the Ross Sea Region of Antarctica generally comprise a surface desert pavement and a seasonally thawed active layer over permafrost. Most soils are formed on regolith such as glacial till or colluvium. Mean annual air temperatures range from -18°C to -24°C with low precipitation. The active layer ranges in depth from minimal in higher altitude, colder sites, to near 1 m deep at warmer coastal sites in the northern part of the region. Underlying permafrost may be ice-cemented, or dry with no ice cement. In some areas ice-cored moraine occurs where there is a large body of ice within the subsoil permafrost. Two examples of active gully/fan -forming events, one at Cape Evans and one at Lake Vanda are described. At the Cape Evans event water from a small lake thawed and came into contact with the ice in the underlying patterned ground ice-wedge causing the ice-wedge to melt and extensive gully erosion to occur. A fan-building event near Lake Vanda in the Wright Valley resulted in erosive and depositional features covering a horizontal distance of about 3 km and an altitudinal range of about 1400 m. Such occasional events, can be attributed to warmer than average summers, and were first described in the Ross Sea Region in the 1970s. The Cape Evans and Lake Vanda events are examples of active, rapid, landscape processes and show that landscapes are not as static as is often assumed.

text: Soil and permafrost in the Ross Sea Region of Antarctica: Stable or dynamic? Soils in the Ross Sea Region of Antarctica generally comprise a surface desert pavement and a seasonally thawed active layer over permafrost. Most soils are formed on regolith such as glacial till or colluvium. Mean annual air temperatures range from -18°C to -24°C with low precipitation. The active layer ranges in depth from minimal in higher altitude, colder sites, to near 1 m deep at warmer coastal sites in the northern part of the region. Underlying permafrost may be ice-cemented, or dry with no ice cement. In some areas ice-cored moraine occurs where there is a large body of ice within the subsoil permafrost. Two examples of active gully/fan -forming events, one at Cape Evans and one at Lake Vanda are described. At the Cape Evans event water from a small lake thawed and came into contact with the ice in the underlying patterned ground ice-wedge causing the ice-wedge to melt and extensive gully erosion to occur. A fan-building event near Lake Vanda in the Wright Valley resulted in erosive and depositional features covering a horizontal distance of about 3 km and an altitudinal range of about 1400 m. Such occasional events, can be attributed to warmer than average summers, and were first described in the Ross Sea Region in the 1970s. The Cape Evans and Lake Vanda events are examples of active, rapid, landscape processes and show that landscapes are not as static as is often assumed.

year: 2016

title: An ashy septingentenarian: the Kaharoa tephra turns 700 (with notes on its volcanological, archaeological, and historical importance)

authors: Lowe, David J.

abstract: Most of us are aware of the basaltic Tarawera eruption on 10th June 1886: the high toll on life (~120 people), landscape devastation, and loss of the Pink and White Terraces. But this was not the first time that Mt Tarawera produced an eruption of importance both to volcanology and human history. This edition of the GSNZ Newsletter marks the 700th anniversary of the Kaharoa eruption – its septingentenary to be precise – which occurred at Mt Tarawera in the winter of 1314 AD (± 12 years) (Hogg et al. 2003) (Fig. 1). The importance of the Kaharoa eruption is at least threefold. (1) It is the most recent rhyolite eruption in New Zealand, and the largest New Zealand eruption volumetrically of the last millennium. (2) The Kaharoa tephra is an important marker horizon in late Holocene stratigraphy and geoarchaeology (Lowe et al. 1998, 2000), and in particular helps to constrain the timing of settlement of early Polynesians in North Island (Newnham et al. 1998; Hogg et al. 2003; Lowe 2011). (3) There is a link between the soils that developed on the Kaharoa tephra, the animal ‘wasting’ disease known as ‘bush sickness’, and the birth of a government soil survey group as an independent organisation (Tonkin 2012).

text: An ashy septingentenarian: the Kaharoa tephra turns 700 (with notes on its volcanological, archaeological, and historical importance) Most of us are aware of the basaltic Tarawera eruption on 10th June 1886: the high toll on life (~120 people), landscape devastation, and loss of the Pink and White Terraces. But this was not the first time that Mt Tarawera produced an eruption of importance both to volcanology and human history. This edition of the GSNZ Newsletter marks the 700th anniversary of the Kaharoa eruption – its septingentenary to be precise – which occurred at Mt Tarawera in the winter of 1314 AD (± 12 years) (Hogg et al. 2003) (Fig. 1). The importance of the Kaharoa eruption is at least threefold. (1) It is the most recent rhyolite eruption in New Zealand, and the largest New Zealand eruption volumetrically of the last millennium. (2) The Kaharoa tephra is an important marker horizon in late Holocene stratigraphy and geoarchaeology (Lowe et al. 1998, 2000), and in particular helps to constrain the timing of settlement of early Polynesians in North Island (Newnham et al. 1998; Hogg et al. 2003; Lowe 2011). (3) There is a link between the soils that developed on the Kaharoa tephra, the animal ‘wasting’ disease known as ‘bush sickness’, and the birth of a government soil survey group as an independent organisation (Tonkin 2012).

year: 2014