Tag: Protein

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Polypeptide Poem by Gillian Gaynor

Download Gillian Gaynor’s Polypeptide Poem for a closer look here!

a mind adrift
finding meaning in peptides
deciphering life

By Gillian Gaynor

Peptides are composed of chains of amino acids—organic molecules, encoded by a triplet combination of nucleotides in a strand of DNA or RNA (codon), that contain a carboxyl group, amino group and characteristic side chain.

A protein’s primary structure is determined by the specific sequence of amino acids in a polypeptide chain while the secondary, tertiary and quaternary structures are held together by intra- and intermolecular interactions and refer to the spatial arrangement and 3D conformation of the chain(s). The hierarchical nature of polypeptide formation and folding is crucial to its function as it allows proteins to perform specific roles in an organism.

Proteins are essential to nearly every biochemical process, serving as enzymes to catalyze reactions, hormones and neurotransmitters to regulate physiological responses, and structural units that contribute to the integrity of cells, tissues and bones, among many other examples.

Further reading:

‘Biochemistry, Peptide’, 2023, Forbes, J. & Krishnamurthy, K., StarPearls Publishing, available: https://www.ncbi.nlm.nih.gov/books/NBK562260/

Author bio:

Gillian Gaynor, a novice poet from Pittsburgh, received her bachelor’s degree in biochemistry from Notre Dame. Currently applying to medical school, Gillian bridges her scientific roots and budding poetic interests by crafting “polypeptide poems”—abstract haikus that challenge the reader to decode the hidden meaning in chains of amino acids.

You can connect with Gillian on LinkedIn here: https://www.linkedin.com/in/gilliangaynor/

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Ant-y-insulin

Long live queens! But why?
Ovaries might change growth cues
to extend lifespan!

By Dr Nathan Woodling

A queen takes the throne.
Insulin surges, eggs grow.
A switch extends life.

By Dr Andrew Holmes

Reproduction is linked to reduced lifespan in many animals, yet ant queens have a far greater longevity compared to workers in their colony – black garden ant queens can live up to 30 times longer than the 1-year lifespan of their workers. Ant queens have the same genome as their workers, and in some species of ant they aren’t reared differently but switch caste following the death of the current queen.

The Indian jumping ant (Harpegnathos saltator) exhibits this switching behaviour. When a queen dies, workers duel each other, with the winners transitioning into pseudo-queens known as gamergates. These gamergates begin laying fertile eggs and their lifespan is substantially increased – from 7 months to 4 years. Gamergates can even transition back into the worker caste if replaced by another queen, their lifespan reverting back to 7 months.

How is ant lifespan so mutable?

New research by Yan et al. (2022) points to an insulin-suppressing protein as a possible answer.

The researchers compared gene expression during caste switching and found that ants that switch from worker to gamergate produce more insulin. The increased insulin results in a change in the balance of activity between the two main insulin signalling pathways, MAPK (which controls metabolism and egg formation) and AKT (which controls ageing).

On transitioning to a gamergate, the MAPK insulin signalling pathway’s activity increases, inducing ovary development and the production of eggs. But this also results in the production of an insulin-suppressing protein (Imp-L2) which blocks the AKT insulin signalling pathway, increasing longevity.

IMP-L2 essentially acts as a switch between a worker being short-lived and sterile compared to a queen being long-lived and fertile.

Original research:

http://dx.doi.org/10.1126/science.abm8767

A note about the sciku:

Nathan and Andrew independently wrote their sciku about this research and discovered the coincidence when Nathen posted his poem on Twitter. The two different approaches to writing about the same subject demonstrate why sciku are such a consistently interesting medium for exploring and sharing research.

Author bios:

Dr Nathan Woodling is a lecturer in molecular biosciences at the University of Glasgow. You can follow him on Twitter here: @NathanWoodling.

Dr Andrew Holmes is a former researcher in animal welfare and the founder and editor of The Sciku Project. You can follow him on Twitter here: @AndrewMHolmes.

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These membrane proteins by Chris Gillen

These membrane proteins

might reclaim salt from urine

or suck it from ponds.

 

Mosquitoes face extraordinary challenges to their salt and water balance during their complex life-cycles. Larva of most species live in freshwater environments in which they lose salt by diffusion and gain water by osmosis. In contrast, adults live in terrestrial environments where water loss is a problem. Finally, female mosquitoes ingest large amounts of salt and water when they take a blood meal.

In vertebrates, the sodium-potassium-chloride cotransporters (NKCCs) participate in both salt secretion and absorption. Whereas secretory roles for this group of transporters are well-described in insects, their roles in salt absorption are less well studied. Piermarini et al (2017) recently identified yellow fever mosquito transport proteins that have sequence similarity to the vertebrate NKCCs. Two of these transporters apparently resulted from gene duplications early in the insect and mosquito lineages, suggesting that they have diverged into roles related to mosquito osmoregulation. The transporters may contribute to salt absorption, because the researchers found them in adult hindgut and larval anal papillae, both tissues that transport salt into the body.

Original research: Piermarini, P. M., Akuma, D. C., Crow, J. C., Jamil, T. L., Kerkhoff, W. G., Viel, K. C. M. F., and Gillen, C. M. (2017) Differential expression of putative sodium-dependent cation-chloride cotransporters in Aedes aegypti. Comp. Biochem. Physiol. A 214, 40-49. https://doi.org/10.1016/j.cbpa.2017.09.007

Chris Gillen teaches animal physiology and science writing at Kenyon College in Gambier, Ohio.  He is author of The Hidden Mechanics of Exercise (Harvard, 2014) and Reading Primary Literature (Pearson, 2007).

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TF gets in on the bud by Jolene Ramsey

Fat tags the protein

To the surface it transits

Wrapped in the virus

Living cells are like microscopic cities. The proteins, which are the workhorses of a cell, must accurately navigate to the place where they will perform their assigned tasks. Sometimes we equate the way that proteins get to their final destination to adding an address to a letter.

When a virus infects a cell, its proteins must conform to the cell norm or rewire the system. It is of interest to understand how viruses approach this problem. In the case of a small accessory protein called TF that is found in the virions of Sindbis virus, adding lipids to the protein serves as its ‘address’ to get it to the location where new virions are released from an infected cell.

Original research: https://dx.doi.org/10.1128%2FJVI.02000-16

During graduate school, Jolene Ramsey studied the molecular mechanisms governing enveloped eukaryotic virus assembly. She has a long-term interest in understanding how viruses exploit host cells to build more virions.  You can follow her on Twitter under the handle @jrrmicro

Enjoyed Jolene’s sciku? Check out her other sciku ‘Click click go!’, ‘Privateer, the phage’, ‘The Phriendly Phage’ and Saba, the morning breeze.

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Egg quality

Low egg quality –

the impact of age. Blocking

proteins slows decline.

 

As women age their reproductive ability decreases due to declining egg quality. However, research by Templeman et al (2018) suggests that blocking a particular group of proteins may help to slow this decline, potentially extending the reproductive period.

The proteins, known as cathepsin B proteases, are more common in age-degraded oocytes (unfertilised eggs) and appear to be part of the problem of decreasing quality. By blocking the proteins in C. elegans worms oocyte quality was maintained for much longer, regardless of whether the drug was administered at the beginning or part way through the worms’ reproductive period. Whilst it’s not ready for testing with humans, it points the way towards an interesting new approach.

Original research: http://dx.doi.org/10.1016/j.cub.2018.01.052

 

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Crop blighter

Rice blast: crop blighter.

Inhibiting one protein

stops the fungal spread.

 

Up to 30% of rice crop is destroyed by rice blast every year, causing huge welfare and economic costs. Sakulkoo et al (2018) have found that inhibiting a single protein enzyme in the fungus stops the spread of the blight through a rice plant.

The fungus’s mitogen-activated protein Pmk1 plays a role in suppressing its host’s immune system and controls the ability of the fungus to move from one rice cell to another. By inhibiting Pmk1’s kinase the fungus is trapped within the infected rice cell and is unable to spread and infect the rest of the rice plant. This latest discovery could point the way towards new rice blast control methods, resulting in increased food security and economic development.

Original research: http://dx.doi.org/10.1126/science.aaq0892

 

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Transcription by Prof Sridhar Hannenhalli

To express or not

Here now a bit or a lot

That is the question.

 

Every cell in an organism contains an identical copy of the genome, except for rare somatic mutations, that encodes its entire gene complement. Yet, each of the hundreds of individual cell types in an organism utilizes a well-defined subset of the genes – imagine your neurons expressing genes that are normally expressed in skin cells. Thus the cell, starting from the single-celled embryo, must have a mechanism to control when, and how much of, each gene is expressed. This control is exercised, in large part, at the level of transcription – the process of reading the DNA encoding a gene on the genome and copying it into a messenger RNA (mRNA), which is eventually translated into the final protein product (or otherwise processed into a final RNA product).

Besides controlling normal development and defining the identity of individual cells, the response to a change in environment is also managed at the level of transcription.  This was first demonstrated by Jacques Monod and Francois Jacob in their seminal 1961 paper, showing that a group of E. coli genes that encode for proteins required to break down lactose is transcriptionally switched on or off depending on whether the growth medium is rich in lactose or glucose. They went on to win the 1965 Nobel Prize in Physiology or Medicine for their discovery.

Transcriptional control plays a critical role not only in development and environmental response, but also at a longer time scale in mediating evolutionary divergence across species. In their classic 1975 paper, Mary-Claire King and Alan C Wilson, observing very high levels of similarity between several proteins of chimpanzees and humans, concluded that the vast phenotypic differences between the two species could not be explained by such small degree of molecular divergence and are likely to be driven by the changes in the mechanisms controlling the gene transcription.

The role of transcriptional control in dictating natural diversity at multiple natural scales from cells within an organism, individuals within a species, and across species is now well established. This extends even to phenotypic changes associated with all complex diseases, and is underscored by the observation that the vast majority of genotypic signals associated with human diseases reside in non-protein-coding regions of the genome, thus focusing the research efforts in interpreting these signals in the context of transcriptional control.

Original research:

Jacob, F. & Monod, J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3, 318–356.  http://biotheory.phys.cwru.edu/phys320/JacobMonod1961.pdf

King, M. C. & Wilson, A. C. (1975) Evolution at two levels in humans and chimpanzees. Science (80) 188, 107–116. https://doi.org/10.1126/science.1090005

Hindorff, L. A. et al. (2009)Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. PNAS 106, 9362–9367.  https://doi.org/10.1073/pnas.0903103106

Sridhar Hannenhalli is professor of Cell Biology and Molecular Genetics at the UMD, interested in transcriptional regulation and evolution. He is currently visiting IISc, Bangalore, as a Fulbright scholar. You can follow him on twitter @hannenhalli.

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Ancestral origami

To fold life’s proteins:

Ancestral origami

around hockey pucks.

 

The basic way DNA is stored within cells is remarkably conserved suggesting a deep ancestral origin. Mattiroli et al (2017) have revealed that the way DNA is folded in eukaryotes (a domain containing animals, plants, fungi and protists) is very similar to the way its folded in archaea, a domain of single-celled microorganisms containing some of the oldest forms of life.

In both eukaryotes and archaea DNA is wrapped around proteins called histones creating the same DNA geometry. This suggests that eukaryote DNA folding method is ancestral, although a key difference is that in eukaryotes DNA is wrapped around bundles of 8 histones (sometimes referred to as a ‘hockey puck’) whilst in archaea its just wrapped around individual histones.

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Tiny passengers

What will satisfy

these cravings? I should ask my

tiny passengers.

 

Choosing what and how much to eat is crucial as even those nutrients that are normally beneficial can be harmful if consumed excessively. But the mechanism for how animals regulate the amount they eat isn’t always clear.

The common fruit fly develops a strong appetite for amino acid-rich food if fed a diet lacking in certain essential amino acids, and the fly’s reproductive effort will also decrease. However, this change in appetite and reproduction is suppressed if the fly has certain species of gut bacteria. Interestingly, when given the choice fruit flies will eat more food that contains these bacteria than food that doesn’t suggesting an ability of the flies to direct their own gut bacterial microbiome.

How the bacteria influence fruit fly behaviour and physiology is uncertain but results suggest that it is not down to the bacteria producing the missing amino acids for the flies or that the flies are consuming the bacteria themselves. Possible explanations are that the bacteria secrete metabolites that help the flies use their remaining amino acids more effectively or that the bacteria directly modulate the flies own nutrient sensing pathways so that the flies don’t recognise a decrease in amino acids. Leitão-Gonçalves et al, 2017.