The Sunday Papers

April 23rd

Recent Publications Harnessing the Power of Translatomics.

Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.

In this week’s Sunday papers, Li et al. look at the role of translation in locust phase transition, Hadjeras et al. look at unveiling the small proteome in the algae Haloferax volcanii, while Zhang investigate the detoxification role of Chlamydomonas reinhardtii for potential bioremediation applications.

Cytosolic and mitochondrial ribosomal proteins mediate the locust phase transition via divergence of translational profiles

Proceedings of the National Academy of Sciences, 2023
Li, J., Wei, L., Wang, Y., Zhang, H., Yang, P., Zhao, Z. and Kang, L.

Locusts exhibit the ability to transform their physical characteristics in response to fluctuations in population density. This transition from low-density solitary locusts to high-density gregarious locusts is a major contributor to the devastating outbreaks of locust infestations. However, the role of translational regulation remains poorly understood.
In this study, the researchers investigated the molecular mechanisms underlying the locust phase transition. They used polysome profiling and ribosome profiling to compare the translational profiles of solitary and gregarious locusts and found that the two types of locusts exhibit divergent polysome profiles for their cytosolic and mitochondrial ribosomal proteins, leading to different translational strategies.

The researchers found that the expression levels of several cytosolic RPs were significantly upregulated in gregarious locusts compared to solitary ones. In contrast, the expression levels of several mitochondrial RPs were significantly downregulated in gregarious locusts compared to solitary ones. In gregarious locusts, ten genes involved in the cytosolic ribosome pathway exhibited increased translational efficiency (TE). In solitary locusts, five genes from the mitochondrial ribosome pathway displayed increased TE. Furthermore, the researchers identified several transcription factors that were differentially expressed between the two groups, which may play a role in regulating the expression of ribosomal proteins (RPs) and other genes involved in the phase transition.

This study reveals that locusts employ divergent ribosome pathways to cope with changes in population density. These findings also suggest that alterations in transcription factor activity may also mediate the locust phase transition by altering protein synthesis and mitochondrial function. Findings such as these provide important clues in searching for molecular targets for pest control.

Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimised mass spectrometry.

microLife, 2023
Hadjeras, L., Bartel, J., Maier, L.K., Maaß, S., Vogel, V., Svensson, S.L., Eggenhofer, F., Gelhausen, R., Müller, T., Alkhnbashi, O.S. and Backofen, R.

Small ORFs, also known as sORFs, are difficult to predict due to their short length and lack of recognizable protein domains, resulting in their omission from annotations. While prokaryotic “small” transcriptomes have been extensively studied, small proteomes, which include proteins with a length of 70 amino acids or less, have only recently started receiving attention. Unfortunately, inventories of small proteomes remain scarce in archaea.

To address this gap in knowledge, a recent study aimed to identify the small proteome of the archaeon Haloferax volcanii. The researchers used ribosome profiling (Ribo-seq) and small-protein optimized mass spectrometry to detect previously unannotated small proteins. The article first describes the steps needed to adapt the Ribo-seq workflow, and show that RNase I works well for archaea, while the footprints obtained showed a broad distribution in length from 12 to 40 nucleotides with the 27–30 nt footprints being predominant.

Using the complementary approach, both methods allowed the detection of novel sORFs, with an overlapping set of seven sORFs identified. The study found that Ribo-seq tended to detect smaller and more basic proteins compared to MS, which may be due to biases in the MS-based approach. The authors identified 47 strong candidates for novel sORFs, some of which were missed by computational prediction tools.

In total, the study identified 60 previously unknown small proteins involved in various cellular processes. The translation of five of these new small proteins was confirmed by in vivo expression and western blot analysis. Based on these findings, the study concluded that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea. The study provides a valuable first dataset for optimizing algorithms for archaeal data.

Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity.

Journal of Hazardous Materials, 2023
Zhang, B., Tang, Y., Yu, F., Peng, Z., Yao, S., Deng, X., Long, H., Wang, X. and Huang, K. 

Cadmium (Cd) is a harmful contaminant in aquatic ecosystems, threatening human health even at low levels. Microalgae are ideal for bioremediating heavy metal-contaminated wastewater due to their rapid growth and metal binding sites. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about whether Cd impacts at the translational level.

In brief, this study showcases how algae respond to Cd stress. The authors used ribosome profiling to observe changes in the translatome when cells were exposed to Cd. They identified 2953 differentially translated genes, of which 1560 were upregulated and 1393 were downregulated, and categorized them into 18 functional groups using the MapMan database.

The study revealed that Cd exposure caused the differential regulation of many genes associated with cell structure and the cell cycle, with some flagella-related genes being downregulated and cell death-related genes being upregulated. Genes encoding glycoproteins that could potentially bind to Cd and prevent its entry into cells were also upregulated. The formation of palmelloid colonies as a potential strategy to withstand Cd exposure was also noted. It was therefore concluded that morphological modification of algae is a critical strategy for adapting to Cd stress. Translatome analysis also identified redox-related genes, including those involved in the ascorbate-glutathione cycle and H2O2 detoxifying enzymes, playing a role in Cd detoxification. There was an upregulation of VTC2 and GLDH genes as well as the upregulation of GPX and PRX genes indicating an essential role of the ascorbate-glutathione cycle in maintaining reactive oxygen species (ROS) homeostasis in Cd-treated algal cells.

In summary it was shown that Cd disrupts various cellular metabolic processes in C. reinhardtii, however, algae can develop several adaptive mechanisms to cope with this stress, including morphological changes, starch accumulation, and high-electron-density particles. All of which may have implications for the bioremediation of Cd-contaminated water.

Oscar Ting

Oscar Ting

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