Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney

Copeland, Alex; Yasawong, Montri; Lapidus, Alla; Lucas, Susan; Deshpande, Shweta; Pagani, Ioanna; Tapia, Roxanne; Cheng, Jan‐Fang; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Pan, Chongle; Brambilla, Evelyne; Rohde, Manfred; Tindall, Brian J.; Sikorski, Johannes; Göker, Markus; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter; Woyke, Tanja

doi:10.4056/sigs.2435521

“…In contrast, Thorarchaeota AH sampled on 3 continents form a clade suggesting vertical inheritance of MH in Asgard (Supplementary Figure S7A, inset). Considering AH dominance over BH together with evidence of recent HGT of BH genes among Thermales (e.g., plasmid pAA3-7b, Supplementary Figure S7A) and Thiotrichales, which may both share with hyperthermophilic TACK archaea such ecological niche as hydrothermal vents (Copeland et al, 2012;Dombrowski et al, 2017;Scott et al, 2019;Zaremba-Niedzwiedzka et al, 2017), the data suggest BH basal position in MH clade could indicate AH HGT toward bacteria.…”

Section: Mnth H: Archaeal Link Between Bacterial Ma and Eukaryotic Nrampmentioning

confidence: 94%

Nramp: Deprive and conquer?

Cellier

¹

2022

Front. Cell Dev. Biol.

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Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.

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“…No single homolog simultaneously had the highest activity, expression, and specificity, so we chose two parent enzymes: StACSstab because it had the highest k cat , and MhACS (from Marinithermus hydrothermalis ) because it had the highest lysate activity. Both are also likely tolerant to mutation, since StACSstab is computationally stabilized and MhACS comes from a thermophile ( 40 ).…”

Section: Resultsmentioning

confidence: 99%

Enzyme engineering and in vivo testing of a formate reduction pathway

Wang

¹

,

Anderson

²

,

Yang

³

et al. 2021

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Formate is an attractive feedstock for sustainable microbial production of fuels and chemicals, but its potential is limited by the lack of efficient assimilation pathways. The reduction of formate to formaldehyde would allow efficient downstream assimilation, but no efficient enzymes are known for this transformation. To develop a 2-step formate-reduction pathway, we screened natural variants of acyl-CoA synthetase (ACS) and acylating aldehyde dehydrogenase (ACDH) for activity on one-carbon substrates and identified active and highly expressed homologs of both enzymes. We then performed directed evolution, increasing ACDH specific activity by 2.5-fold and ACS lysate activity by 5-fold. To test for in vivo activity of our pathway, we expressed it in a methylotroph which can natively assimilate formaldehyde. Although the enzymes were active in cell extracts, we could not detect formate assimilation into biomass, indicating that further improvement will be required for formatotrophy. Our work provides a foundation for further development of a versatile pathway for formate assimilation.

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“…MhACS (from M. hydrothermalis) because it had the highest lysate activity. Both are also likely tolerant to mutation, since StACSstab is computationally stabilized and MhACS comes from a thermophile (21).…”

Section: Directed Evolution Of Acsmentioning

confidence: 99%

Enzyme engineering andin vivotesting of a formate-reduction pathway

Wang

¹

,

Anderson

²

,

Yang

³

et al. 2021

Preprint

1

0

View full text Add to dashboard Cite

Formate is an attractive feedstock for sustainable microbial production of fuels and chemicals, but its potential is limited by the lack of efficient assimilation pathways. The reduction of formate to formaldehyde would allow efficient downstream assimilation, but no efficient enzymes are known for this transformation. To develop a 2-step formate-reduction pathway, we screened natural variants of acyl-CoA synthetase (ACS) and acylating aldehyde dehydrogenase (ACDH) for activity on one-carbon substrates and identified active and highly expressed homologs of both enzymes. We then performed directed evolution, increasing ACDH specific activity by 2.5-fold and ACS lysate activity by 5-fold. To test for in vivo activity of our pathway, we expressed it in a methylotroph which can natively assimilate formaldehyde. Although the enzymes were active in cell extracts, we could not detect formate assimilation into biomass, indicating that further improvement will be required for formatotrophy. Our work provides a foundation for further development of a versatile pathway for formate assimilation.

show abstract

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney

Cited by 9 publications

References 35 publications

Nramp: Deprive and conquer?

Nramp: Deprive and conquer?

Enzyme engineering and in vivo testing of a formate reduction pathway

Enzyme engineering andin vivotesting of a formate-reduction pathway

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