Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins

Garcia, Amanda K.; Kolaczkowski, Bryan; Kaçar, Betül

doi:10.1101/2021.07.07.451390

Cited by 4 publications

(5 citation statements)

References 81 publications

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“…The only problem with figure 4 A is that Groups I, II, and III NifD sequences are clustered with Groups II and III NifE sequences. Only this part of figure 4 A supports the NifEN-first hypothesis, which postulates that NifEN were the ancestral sequences and that NifDK were a duplication of NifEN (GBE 2022; Garcia et al 2022 ).…”

Section: Resultsmentioning

confidence: 68%

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Origin and Evolution of Nitrogen Fixation in Prokaryotes

Lin

Chen

et al. 2022

Molecular Biology and Evolution

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The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing bacteria are far larger in number and far more diverse in ecological niches than nitrogen-fixing archaea. We therefore propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six nitrogen-fixing (Nif) proteins individually or in combination. In each of these trees the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of nitrogen-fixing archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.

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Section: Resultsmentioning

confidence: 68%

“…5 A and B ) and that in both figure 5 A and B Group IV includes no NifE and NifN sequences. These two observations were not made by Garcia et al (2022) , because their study included no Group IV NifD and NifK sequences.…”

Section: Resultsmentioning

confidence: 99%

Origin and Evolution of Nitrogen Fixation in Prokaryotes

Lin

Chen

et al. 2022

Molecular Biology and Evolution

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“…Biological nitrogen fixation (diazotrophy)-the reduction of atmospheric dinitrogen gas (N 2 ) to ammonia (NH 3 ) with concomitant hydrogen gas (H 2 ) production-is a critical source of bioavailable nitrogen for living organisms [14][15][16] . The key enzymes mediating this process are nitrogenases, which include three forms distinguished by their active site metal cofactors: molybdenum-iron nitrogenase Nif (Mo-Fe), vanadium-iron nitrogenase Vnf (V-Fe) and iron-only nitrogenase Anf (Fe-Fe) 17,18 .…”

mentioning

confidence: 99%

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

et al. 2022

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Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.

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“…To minimize bias of the method, different alignment algorithms were used to generate alternative trees following Garcia et al 79 The combined phylogeny of IF2 and EF‐Tu was constructed using the same 408 IF2 and 408 EF‐Tu sequences. In total, 816 sequences were aligned together using MAFFT L‐INS‐i 35 and MUSCLE v3.8 alignment 80 .…”

Section: Methodsmentioning

confidence: 99%

Early divergence of translation initiation and elongation factors

et al. 2022

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Protein translation is a foundational attribute of all living cells. The translation function carried out by the ribosome critically depends on an assortment of protein interaction partners, collectively referred to as the translation machinery. Various studies suggest that the diversification of the translation machinery occurred prior to the last universal common ancestor, yet it is unclear whether the predecessors of the extant translation machinery factors were functionally distinct from their modern counterparts. Here we reconstructed the shared ancestral trajectory and subsequent evolution of essential translation factor GTPases, elongation factor EF-Tu (aEF-1A/eEF-1A), and initiation factor IF2 (aIF5B/eIF5B). Based upon their similar functions and structural homologies, it has been proposed that EF-Tu and IF2 emerged from an ancient common ancestor. We generated the phylogenetic tree of IF2 and EF-Tu proteins and reconstructed ancestral sequences corresponding to the deepest nodes in their shared evolutionary history, including the last common IF2 and EF-Tu ancestor. By identifying the residue and domain substitutions, as well as structural changes along the phylogenetic history, we developed an evolutionary scenario for the origins, divergence and functional refinement of EF-Tu and IF2 proteins. Our analyses suggest that the common ancestor of IF2 and EF-Tu was an IF2-like GTPase protein. Given the central importance of the translation machinery to all cellular life, its earliest evolutionary constraints and trajectories are key to characterizing the universal constraints and capabilities of cellular evolution.

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Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins

Cited by 4 publications

References 81 publications

Origin and Evolution of Nitrogen Fixation in Prokaryotes

Origin and Evolution of Nitrogen Fixation in Prokaryotes

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

Early divergence of translation initiation and elongation factors

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