Net Charges of the Ribosomal Proteins of the
            <i>S10</i>
            and
            <i>spc</i>
            Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Tirumalai, Madhan R.; Anane-Bediakoh, Daniela; Rajesh, Sidharth; Fox, George E.

doi:10.1128/spectrum.01782-21

Cited by 3 publications

(4 citation statements)

References 117 publications

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“…Classical operons are found to occur in both Bacteria and Archaea [84,85]. The conservation of the arrangement of the r-protein gene cluster is in congruence with how they are conserved in sequence [21,22,55]. A large chunk of 14 genes from the most highly conserved S10-spc cluster of r-protein coding genes was thus found to be similarly conserved in arrangement, whether it was Bacteria, Asgard, or non-Asgard Archaea.…”

Section: Discussionmentioning

confidence: 73%

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Ribosomal Protein Cluster Organization in Asgard Archaea

Tirumalai,

Sivaraman,

Kutty

et al. 2023

Archaea

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It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.

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Section: Discussionmentioning

confidence: 73%

“…In general, we will refer to them as clusters with the implication that many of them could likely be operons. The S10 and the spc operons (clusters) are the largest, each typically encoding ten-twelve r-proteins [21,22]. Gene expression when known is frequently regulated by one of the r-protein components within the cluster.…”

Section: Introductionmentioning

confidence: 99%

Ribosomal Protein Cluster Organization in Asgard Archaea

Tirumalai,

Sivaraman,

Kutty

et al. 2023

Archaea

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“…As an outcome of such active engagement in EPO, such experiences have helped in maintaining a strong track record of supporting and mentoring minority, high school, undergraduate, and beginning graduate students. When their contributions have been substantial, they have been included as co-authors in peer-reviewed publications ( 41 , 42 , 56 , 60 , 61 ).…”

Section: Methodsmentioning

confidence: 99%

Education and public outreach: communicating science through storytelling

Tirumalai

2024

J Microbiol Biol Educ.

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Education and public outreach activities can be challenging for most active scientists, for very good reasons. Allotment of time to participate in outreach activities could be a major challenge. However, when such activities are incorporated into one’s academic and research plan, they can be enriching. Here, the author describes his experience in what began as on one-off participation at an outreach event, leading to a series of speaking events addressing the public at the monthly meetings of several astronomy clubs/societies, observatories, etc. in the states of Texas, Louisiana, New Mexico, and Colorado. They have often involved the use of motifs and characters from popular science fiction, literature, and movies and when possible, getting the audience actively involved in the presentations. Furthermore, the discussions following each presentation have been enriching in terms of getting a broad perspective of the perceptions that people in general have, regarding the origins of life, microbiology, extremophiles, and astrobiology.

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“…Previous studies found that ribosomal genes contain some information about a given organism’s optimal growth temperature and halotolerance ( 13–23 ). For instance, thermophilic ribosomal proteins were found to have a higher content of certain amino acids, such as arginine, isoleucine, proline and tyrosine, and a decreased content of serine and threonine.…”

Section: Introductionmentioning

confidence: 99%

Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA

Elzen

Helena-Bueno

Brown

et al. 2023

Nucleic Acids Research

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Ribosomal genes are widely used as ‘molecular clocks’ to infer evolutionary relationships between species. However, their utility as ‘molecular thermometers’ for estimating optimal growth temperature of microorganisms remains uncertain. Previously, some estimations were made using the nucleotide composition of ribosomal RNA (rRNA), but the universal application of this approach was hindered by numerous outliers. In this study, we aimed to address this problem by identifying additional indicators of thermal adaptation within the sequences of ribosomal proteins. By comparing sequences from 2021 bacteria with known optimal growth temperature, we identified novel indicators among the metal-binding residues of ribosomal proteins. We found that these residues serve as conserved adaptive features for bacteria thriving above 40°C, but not at lower temperatures. Furthermore, the presence of these metal-binding residues exhibited a stronger correlation with the optimal growth temperature of bacteria compared to the commonly used correlation with the 16S rRNA GC content. And an even more accurate correlation was observed between the optimal growth temperature and the YVIWREL amino acid content within ribosomal proteins. Overall, our work suggests that ribosomal proteins contain a more accurate record of bacterial thermal adaptation compared to rRNA. This finding may simplify the analysis of unculturable and extinct species.

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Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Cited by 3 publications

References 117 publications

Ribosomal Protein Cluster Organization in Asgard Archaea

Ribosomal Protein Cluster Organization in Asgard Archaea

Education and public outreach: communicating science through storytelling

Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA

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